ClinVar Miner

Submissions for variant NM_002693.3(POLG):c.1760C>T (p.Pro587Leu)

gnomAD frequency: 0.00160  dbSNP: rs113994096
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Total submissions: 52
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000193529 SCV000248555 pathogenic not specified 2019-07-24 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000427845 SCV000331603 pathogenic not provided 2017-10-05 criteria provided, single submitter clinical testing
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV000415307 SCV000492823 pathogenic Global developmental delay 2014-07-15 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000427845 SCV000511317 pathogenic not provided 2016-08-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000408293 SCV000543885 uncertain significance Progressive sclerosing poliodystrophy 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 587 of the POLG protein (p.Pro587Leu). This variant is present in population databases (rs113994096, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with autosomal recessive POLG-related conditions, and in almost all cases it was observed on the same chromosome (in cis) with a second (p.Thr251Ile) variant (PMID: 12210792, 14635118, 15349879, 16621917, 19189930, 21880868, 25660390). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. To date, the p.Pro587Leu variant has not been observed independent from the p.Thr251Ile variant in individuals with autosomal recessive POLG-related conditions. ClinVar contains an entry for this variant (Variation ID: 13505). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt POLG protein function. Experimental studies have shown that this missense change affects POLG function (PMID: 28154168). In summary, this is a rare variant that is almost always observed in cis with a second variant. It has been shown to segregate with disease, and has also been observed in many individuals with sporadic disease. However, because it almost always occurs in cis with p.Thr251Ile, the individual contribution of this variant to disease cannot be disambiguated. For these reasons, this change has been classified as a Variant of Uncertain Significance.
Athena Diagnostics RCV000427845 SCV000614707 pathogenic not provided 2019-04-16 criteria provided, single submitter clinical testing This variant is seen in cis with POLG c.752C>T (p.Thr251Ile), and the pathogenicity assessment is based on data for NM_002693.2:c.752C>T(;)1760C>T.
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München RCV000186576 SCV000680342 pathogenic Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 2017-11-08 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000020473 SCV000746435 pathogenic Mitochondrial DNA depletion syndrome 1 2017-12-03 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000427845 SCV000802089 uncertain significance not provided 2023-05-09 criteria provided, single submitter clinical testing PP3, PM2, PS3_moderate
Ambry Genetics RCV002313709 SCV000847670 pathogenic Inborn genetic diseases 2021-07-13 criteria provided, single submitter clinical testing The c.1760C>T (p.P587L) alteration is located in exon 10 (coding exon 9) of the POLG gene. This alteration results from a C to T substitution at nucleotide position 1760, causing the proline (P) at amino acid position 587 to be replaced by a leucine (L). Based on the available evidence, the c.1760C>T (p.P587L) alteration is classified as pathogenic for autosomal recessive POLG-related mitochondrial disorders; however, it is unlikely to be causative of autosomal dominant progressive external ophthalmoplegia. Based on data from the Genome Aggregation Database (gnomAD), the POLG c.1760C>T alteration was observed in 0.15% (433/281158) of total alleles studied, with a frequency of 0.26% (341/128840) in the European (non-Finnish) subpopulation. This mutation has been reported to occur almost exclusively in cis with p.T251I (c.752C>T) and this syntenic mutation combination accounts for approximately 6% of all disease causing alleles in POLG (Tang, 2011). This syntenic mutation combination has been detected alone, in trans with various other POLG mutations and alterations, and as homozygous, in individuals with Alpers syndrome, autosomal recessive external ophthalmoplegia (arPEO), neuropathy, myopathy, MNGIE, intellectual disability, and various other POLG-deficiency symptoms (Van Goethem, 2003; Uusimaa, 2013; Weiss, 2010; Horvath, 2006; Tang, 2011). Of note, this mutation has been detected without p.T251I in conjunction with the p.R853W alteration (phase was not confirmed) in an individual with PEO, ptosis, and multiple mtDNA deletions (González-Vioque, 2006). Biochemical characterization of P587L mutant revealed impaired DNA binding affinity, reduced thermostability, diminished exonuclease activity, defective catalytic activity, and compromised DNA processivity; T251I+P587L double mutant showed synergistic effect and had more severe dysfunction than P587L alone (DeBalsi, 2017). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000427845 SCV000884404 likely pathogenic not provided 2018-04-06 criteria provided, single submitter clinical testing
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine RCV000408293 SCV000886904 pathogenic Progressive sclerosing poliodystrophy 2018-10-01 criteria provided, single submitter clinical testing The NM_002693.2:c.1760C>T (NP_002684.1:p.Pro587Leu) [GRCH38: NC_000015.10:g.89325639G>A] variant in POLG gene is interpretated to be a Pathogenic based on ACMG guidelines (PMID: 25741868). This variant has been reported in PMID:15349879 ; 12825077 . This variant meets the following evidence codes reported in the ACMG-guideline. PS1:This variation causes same amino-acid change as an established pathogenic variant. PS3:Well established functional studies show a deleterious effect on POLG. PM2:This variant is absent in key population databases. PM3:Detected in trans with a pathogenic variant for Mitochondrial DNA depletion syndrome 4A (Alpers type) which is a recessive disorder. PP1:This variant is co-segregated with Mitochondrial DNA depletion syndrome 4A (Alpers type) in multiple affected family members. PP2:This is a missense variant in POLG with a low rate of benign and high rate of pathogenic missense variations. PP4:Patient's phenotype or family history is highly specific for POLG. Based on the evidence criteria codes applied, the variant is suggested to be Pathogenic.
Mendelics RCV000408293 SCV001139681 uncertain significance Progressive sclerosing poliodystrophy 2019-05-28 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000427845 SCV001149568 pathogenic not provided 2024-04-01 criteria provided, single submitter clinical testing POLG: PM3:Very Strong, PM2:Supporting, PS3:Supporting
Baylor Genetics RCV001004602 SCV001163772 pathogenic Progressive sclerosing poliodystrophy; Mitochondrial DNA depletion syndrome 4b criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000427845 SCV001446808 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Knight Diagnostic Laboratories, Oregon Health and Sciences University RCV000408293 SCV001448887 likely pathogenic Progressive sclerosing poliodystrophy 2019-01-10 criteria provided, single submitter clinical testing
Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris RCV001642226 SCV001519175 pathogenic Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis 2021-01-04 criteria provided, single submitter research
Baylor Genetics RCV000408293 SCV001529893 pathogenic Progressive sclerosing poliodystrophy 2024-03-26 criteria provided, single submitter clinical testing
Kariminejad - Najmabadi Pathology & Genetics Center RCV001813986 SCV001755620 pathogenic Abnormality of the nervous system 2021-07-10 criteria provided, single submitter clinical testing
Genomics England Pilot Project, Genomics England RCV000408293 SCV001760353 likely pathogenic Progressive sclerosing poliodystrophy criteria provided, single submitter clinical testing
Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino RCV001610290 SCV001832553 pathogenic Tip-toe gait 2021-02-10 criteria provided, single submitter clinical testing c.1760C>T p.(Pro587Leu) [dbSNP: rs113994096, Frequenz: A=0.15%, GnomAD] is rated by the majority (15 entries) as "probably pathogenic" and "pathogenic" in the ClinVar mutation database. Hereditary motor sensory neuropathy (HMSN), also known as Charcot-Marie-Tooth Disease (CMT), is the most commonly inherited peripheral polyneuropathy. It constitutes a group of inherited, progressive, motor and sensory peripheral nerve disorders with properties of demyelination, axonal degeneration, or both. It is classified by clinical characteristics, modes of inheritance, electrophysiologic features, metabolic defects, and specific gene markers. Our patients all walk on tiptoe, so they show similar symptoms. When we genetically test them with our toe walking panel, we find that around 90 per cent of them have a genetic variant that explains their toe walking. These can be assigned, for example, to the area of myopathies (such as variants of the COL6A3 gene), the area of hereditary neuropathies (such as variants of the KMT2C gene) or the area of metabolic diseases (such as variants of the PYGM gene). In a smaller group of patients with almost identical symptoms, no abnormality is found in the genes of our panel, but spastic paraplegia can be detected. In another small group of our toe walkers, no abnormalities can be detected in the genes analysed in our toe walking panel, nor do they suffer from spastic paraplegia, as is also the case with healthy children. In contrast to these, however, they show a tiptoe gait. These patients suffer from infantile cerebral palsy, in which toe walking can also be observed.
Institute of Human Genetics, University of Leipzig Medical Center RCV000014456 SCV001950111 uncertain significance Mitochondrial DNA depletion syndrome 4b 2021-07-27 criteria provided, single submitter clinical testing Despite strong evidence for its pathogenicity, this variant has to be classified as of unknown significance, according to the ACMG-criteria (Richards et al., 2015)
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV000427845 SCV002011121 likely pathogenic not provided 2021-11-03 criteria provided, single submitter clinical testing
DASA RCV001813743 SCV002061213 pathogenic POLG-related disorder 2022-01-05 criteria provided, single submitter clinical testing The c.1760C>T;p.(Pro587Leu) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 13505; OMIM 174763.0011; PMID: 12825077; 25660390; 12975295; 1539879; 19578034; 24265579; 23448099;25742477; 26224072) - PS4.The p.(Pro587Leu) was detected in trans with a pathogenic variant (PMID: 19578034) - PM3. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. The variant was observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern (PMID: 25660390) - BP2. In summary, the currently available evidence indicates that the variant is pathogenic.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001847603 SCV002105557 likely pathogenic Hereditary spastic paraplegia 2021-11-22 criteria provided, single submitter clinical testing
AiLife Diagnostics, AiLife Diagnostics RCV000427845 SCV002503521 likely pathogenic not provided 2022-03-28 criteria provided, single submitter clinical testing
Institute of Human Genetics, University Hospital Muenster RCV004584326 SCV002506434 uncertain significance See cases 2021-12-08 criteria provided, single submitter clinical testing ACMG categories: PM1,PM2,PP3,BP1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV001004602 SCV002512294 pathogenic Progressive sclerosing poliodystrophy; Mitochondrial DNA depletion syndrome 4b 2022-02-15 criteria provided, single submitter clinical testing ACMG classification criteria: PS3 supporting, PS4 strong, PS4, PM3 strong, PP3 supporting
Genetics and Molecular Pathology, SA Pathology RCV000014456 SCV002556643 likely pathogenic Mitochondrial DNA depletion syndrome 4b 2023-04-05 criteria provided, single submitter clinical testing The POLG c.1760C>T variant is classified as LIKELY PATHOGENIC (PS3, PS4_moderate, PP1_moderate, PP3) This sequence change in exon 10 of 23 replaces proline with leucine at codon 587 of the POLG protein (p.Pro587Leu). This variant is present in population databases (gnomAD 232/152196 heterozygotes, 0 homozygote). The variant has been reported in dbSNP (rs113994096). The variant has been reported with conflicting interpretations of pathogenicity by other diagnostic laboratories (ClinVar Variation ID: 13505). Computational predictions support a deleterious effect on the gene or gene product (PP3). The variant has been reported in many individuals affected with POLG-related diseases, and in almost all cases it has been observed on the same chromosome (in cis) with the second (p.Thr251Ile) variant also detected in this patient (PMID: 25660390, 14635118, 15349879, 16621917, 19189930, 21880868) (PS4_moderate). In many of these previously reported cases, the two variants in cis were observed on the opposite chromosome (in trans) from a third, pathogenic variant in an affected individual. The p.Pro587Leu and p.Thr251Ile variant combination in cis accounts for approximately 6% of disease-causing alleles in POLG-related disorders, mainly in Caucasians (PMID: 21880868). The p.Pro587Leu and Thr251Ile variants in cis have been reported to segregate with disease in several families (PMID: 12210792, 15349879) (PP1_moderate). Functional studies of the Thr251Ile and Pro587Leu variants revealed impaired DNA binding affinity, reduced thermostability, diminished exonuclease activity, defective catalytic activity and compromised DNA processivity; the Thr251Ile+Pro587Leu double variant showed a synergistic effect and had more severe dysfunction than the either of the variants alone (PMID: 28154168) (PS3). NO THIRD POLG variant was detected in this patient
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV001813743 SCV002568173 pathogenic POLG-related disorder 2022-06-02 criteria provided, single submitter clinical testing PS3, PM3_Strong, PP1, PP3
3billion RCV000186576 SCV002572626 likely pathogenic Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 2022-09-01 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.154%). Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.80; 3Cnet: 0.93). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000013505). The variant was observed in cis with NM_002693.3:c.752C>T (p.Thr251Ile) in many individuals affected with POLG-related diseases (PMID: 25660390, 14635118, 15349879, 16621917, 19189930, 21880868). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.
MGZ Medical Genetics Center RCV000186576 SCV002581640 pathogenic Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 2022-07-29 criteria provided, single submitter clinical testing
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill RCV000186576 SCV002587017 pathogenic Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 2021-07-27 criteria provided, single submitter research
Genetic Medico-Diagnostic Laboratory Genica RCV002319424 SCV002605540 pathogenic Hypertrophic cardiomyopathy 2022-10-19 criteria provided, single submitter clinical testing The variant was classified as pathogenic according to the ACMG Guidelines, 2015. The variant was found with an allele frequency of 0.1540% (one reported homozygote) in the control populations from the gnomAD v2.1.1 project. In silico analysis by Polyphen-2, SIFT and Mutation-Taster predicted it as damaging. The amino acid change is in a highly conserved position and proline and leucine have moderate physicochemical difference. The variant was identified in cis with variant POLG(NM_002693.3):c.752C>T in a patient with Hypertrophic cardiomyopathy. The patient is also carrier of variants GTPBP3(NM_032620.4):c.181G>C and GTPBP3(NM_032620.4):c.1199C>T in compound heterozygous state.
Institute of Human Genetics, University of Leipzig Medical Center RCV001813743 SCV003804668 likely pathogenic POLG-related disorder 2022-12-19 criteria provided, single submitter clinical testing _x000D_Criteria applied: PS3, PS4_SUP, PP3, PP1
Revvity Omics, Revvity RCV000427845 SCV003818479 pathogenic not provided 2023-07-11 criteria provided, single submitter clinical testing
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV000014456 SCV003843876 likely pathogenic Mitochondrial DNA depletion syndrome 4b 2021-02-13 criteria provided, single submitter clinical testing A heterozygous missense variation in exon 10 of the POLG gene that results in the amino acid substitution of Leucine for Proline at codon587 was detected. The observed variant c.1760C>T (p.Pro587Leu) has a minor allele frequancy of 0.08% and 0.1% in the 1000 genomes and gnomAD databases. The in silico prediction of the variant is damaging by PolyPhen-2 (HumDiv), SIFT, LRT and MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as likely pathogenic.
Illumina Laboratory Services, Illumina RCV001813743 SCV004801567 pathogenic POLG-related disorder 2021-06-17 criteria provided, single submitter clinical testing The POLG c.1760C>T p.(Pro587Leu) missense variant is well described in the literature and has been reported in individuals with a phenotype consistent with POLG-related spectrum disorders (Van Goethem et al., 2003; Filosto et al. 2003; Lamantea et al. 2004; Wong et al., 2008; Ashley et al., 2008; Burusnukul et al. 2009; Weiss et al. 2010; Tang et al. 2011; Horvath et al., 2006; Dames et al. 2013; Helbling et al. 2013; Uusimaa et al. 2013). In almost all of the reported cases, the p.Pro587Leu variant was found in cis with p.Thr251Ile as the complex allele [p.Thr251Ile; p.Pro587Leu]. In an additional two individuals, the p.Pro587Leu variant was found as part of a complex allele with a p.Pro589Leu variant. The p.Pro587Leu variant has also been reported independently in three individuals from the same family in a heterozygous state displaying a dominant pattern of inheritance. Euro et al. (2011) assessed the structure-function relationships of variants in the POLG gene and reported that the p.Pro587Leu variant constrains the Beta-hairpin loop between the IP and AID subdomains and postulate it likely reduces processivity as a result of misalignment of the ptDNA with respect to the catalytic site. DeBalsi et al. (2017) investigated the biochemical properties of purified recombinant Pol gamma p.Pro587Leu protein expressed using the baculovirus Sf9 system. Experiments demonstrated that the p.Pro587Leu variant caused a two-fold reduction in DNA binding affinity and significantly reduced thermostability. The catalytic efficiency of the p.Pro587Leu protein was reduced to approximately 32% of the wildtype level. The [p.Thr251Ile; p.Pro587Leu] variant protein demonstrated a more severe catalytic dysfunction, retaining 5% activity compared to the wild type protein and suggesting that these two variants have a synergistic effect. Based on the collective evidence the p.Pro587Leu variant is classified as pathogenic when found as part of a complex allele and of uncertain significance when found independently.
Breakthrough Genomics, Breakthrough Genomics RCV000408293 SCV005088880 pathogenic Progressive sclerosing poliodystrophy 2021-02-18 criteria provided, single submitter clinical testing The missense variant p.Pro587Leu has been previously reported in multiple studies with p.Thr251Ile and reported as disease-causing alleles in patients with POLG-related diseases with a wide range of phenotypes [PMIDs: 25660390, 21880868, 19189930, 16621917, 14635118 and 15349879]. In addition, these two variants were found to be in-cis and co-segregated with disease phenotype in several families [PMID: 25660390, 19189930]. Additionally, in-vitro biochemical characterization showed that individually both p.Thr251Ile and p.Pro587Leu substitutions functionally impair pol γ activity. However, results also suggest a synergistic effect in terms of impaired DNA binding affinity, reduced thermostability, diminished exonuclease activity, defective catalytic activity, and compromised DNA processivity in the double mutant cells suggesting the pathogenicity of these variants [PMID: 28154168]. The heterozygous p.T251I+p.P587L (cis) allele reported to be associated with a relatively mild phenotype and reported as most common recessive mutation in POLG-related phenotypes [PMID: 18546365, 15689359].
Clinical Genetics Laboratory, Skane University Hospital Lund RCV000427845 SCV005197249 pathogenic not provided 2024-01-04 criteria provided, single submitter clinical testing
OMIM RCV000014456 SCV000034706 pathogenic Mitochondrial DNA depletion syndrome 4b 2004-09-01 no assertion criteria provided literature only
GeneReviews RCV000508752 SCV000040907 not provided Mitochondrial disease no assertion provided literature only
OMIM RCV000186576 SCV000240152 pathogenic Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 2004-09-01 no assertion criteria provided literature only
Division of Human Genetics, Children's Hospital of Philadelphia RCV000408293 SCV000536728 pathogenic Progressive sclerosing poliodystrophy 2016-12-12 no assertion criteria provided research
Wellcome Centre for Mitochondrial Research, Newcastle University RCV000508752 SCV000575915 pathogenic Mitochondrial disease 2017-04-07 no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000427845 SCV001740685 pathogenic not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000427845 SCV001807948 pathogenic not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000427845 SCV001926715 pathogenic not provided no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000427845 SCV001952060 likely pathogenic not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000427845 SCV001971389 pathogenic not provided no assertion criteria provided clinical testing
GenomeConnect - Brain Gene Registry RCV003458332 SCV004176863 not provided Progressive sclerosing poliodystrophy; Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1; Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis; Mitochondrial DNA depletion syndrome 4b no assertion provided phenotyping only Variant classified as Pathogenic and reported on 04-20-2016 by Children's National Medical Center. This variant was identified in multiple related participants enrolled in GenomeConnect. Phenotypic data from the proband has been submitted with this variant. Additional phenotypic information for family members might be available from GenomeConnect. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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