Submissions for variant NM_000277.3(PAH):c.441+5G>T

gnomAD frequency: 0.00001  dbSNP: rs62507321

Total submissions: 17

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PAH Variant Curation Expert Panel	RCV000150089	SCV000852117	pathogenic	Phenylketonuria	2018-05-24	reviewed by expert panel	curation	The c.441+5G>T variant in PAH has been reported on >17 PKU alleles (BH4 deficiency excluded). (PP4_Moderate; PMID: 17935162; PMID: 23514811). This variant has an extremely low allele frequency (0.00002886) in gnomAD (PM2; http://gnomad.broadinstitute.org). This variant has 0% enzyme activity (PS3; http://www.biopku.org). This variant was detected in trans with IVS10-11g>a and p.V388M (Pathogenic in ClinVar) (PM3_Strong; PMID: 23514811). Computational prediction tools and conservation analysis suggest that the c.441+5G>T variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PS3, PM3_Strong
Eurofins Ntd Llc (ga)	RCV000078521	SCV000110377	pathogenic	not provided	2014-07-22	criteria provided, single submitter	clinical testing
GeneDx	RCV000078521	SCV000239051	pathogenic	not provided	2022-08-13	criteria provided, single submitter	clinical testing	Many individuals with c.441+5 G>T and another PAH variant were not found to be responsive to tetrahydrobiopterin (BH4), but data are still unclear (Zurfluh et al., 2008; Jeannesson-Thivisol et al., 2015); Not observed at a significant frequency in large population cohorts (gnomAD); Intronic +5 splice site variant in a gene for which loss of function is a known mechanism of disease, and splice predictors support a deleterious effect; This variant is associated with the following publications: (PMID: 31355225, 24296287, 28676969, 9429153, 34426522, 31589614, 33101986, 32778825, 33465300, 33375644, 24941924, 23514811, 25087612, 26481238, 27121329, 26666653)
Fulgent Genetics, Fulgent Genetics	RCV000150089	SCV000611225	pathogenic	Phenylketonuria	2022-04-04	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000150089	SCV000696449	pathogenic	Phenylketonuria	2016-09-29	criteria provided, single submitter	clinical testing	Variant summary: The PAH c.441+5G>T variant involves the alteration of a conserved intronic nucleotide with 4/5 splice prediction tools predicting a significant impact on normal splicing. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 5/121412 (1/24271), which does not exceed the estimated maximal expected allele frequency for a pathogenic PAH variant of 1/126 (0.0079057). Multiple publications cite the variant in affected individuals who are homozygous and compound heterozygous, along with multiple databases/clinical diagnostic laboratories citing the variant as "pathogenic." Therefore, the variant of interest has been classified as Pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000150089	SCV000754087	pathogenic	Phenylketonuria	2025-01-28	criteria provided, single submitter	clinical testing	This sequence change falls in intron 4 of the PAH gene. It does not directly change the encoded amino acid sequence of the PAH protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs62507321, gnomAD 0.01%). This variant has been observed in individual(s) with phenylketonuria or hyperphenylalaninemia (PMID: 9429153, 17502162, 23514811, 23764561, 24296287, 24368688, 24941924, 25596310, 26666653). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 92742). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen	RCV000078521	SCV001250396	pathogenic	not provided	2023-12-01	criteria provided, single submitter	clinical testing	PAH: PM3:Very Strong, PM2, PP4:Moderate, PP3
Revvity Omics, Revvity	RCV000150089	SCV002016496	pathogenic	Phenylketonuria	2021-10-18	criteria provided, single submitter	clinical testing
3billion, Medical Genetics	RCV000150089	SCV002058461	pathogenic	Phenylketonuria	2022-01-03	criteria provided, single submitter	clinical testing	The variant has been reported multiple times as an established pathogenic/likely pathogenic variant (ClinVar ID: VCV000092742). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (BioPKU, PS3_S). In silico prediction tools predicted that this variant influenced pre-mRNA splicing, resulting in aberrant splicing (SPLICEAI: 0.91>=0.8, PP3_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000032, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Baylor Genetics	RCV000150089	SCV004209565	pathogenic	Phenylketonuria	2024-02-24	criteria provided, single submitter	clinical testing
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre	RCV000150089	SCV004804762	pathogenic	Phenylketonuria	2024-03-17	criteria provided, single submitter	research
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000150089	SCV004848711	pathogenic	Phenylketonuria	2022-06-30	criteria provided, single submitter	clinical testing	The c.441+5G>T variant in PAH has been reported in at least 20 individuals with phenylalanine hydroxylase deficiency including at least 12 compound heterozygotes (Zurflüh 2008 PMID: 17935162, Bueno 2013 PMID: 23514811), several of whom presented with classical phenylketonuria (PKU). It has also been identified in 0.0065% (1/15282) of Latino chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has been reported in ClinVar as pathogenic by the ClinGen PAH Variant Curation Expert Panel using the . ACMG-AMP criteria specific for phenylalanine hydroxylase variants (Zastrow 2018 PMID: 30311390) and is curated in the FDA-recognized human genetic variant database (Variation ID 102784). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In vitro functional studies provide some evidence that this variant impacts protein function and decreases PAH activity to 0% (Bueno 2013 PMID: 23514811); however, these types of assays may not accurately represent biological function. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive phenylalanine hydroxylase deficiency. ACMG/AMP Criteria applied: PM2_Supporting, PP3, PP4_Moderate, PM3_VeryStrong, PS3
Mayo Clinic Laboratories, Mayo Clinic	RCV000078521	SCV005414121	pathogenic	not provided	2024-09-03	criteria provided, single submitter	clinical testing	PP3, PM2_moderate, PM3_strong, PS3
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	RCV000078521	SCV000119521	not provided	not provided		no assertion provided	not provided
Counsyl	RCV000150089	SCV000791712	pathogenic	Phenylketonuria	2017-05-30	no assertion criteria provided	clinical testing
Natera, Inc.	RCV000150089	SCV001455107	pathogenic	Phenylketonuria	2020-09-16	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004739341	SCV005361509	pathogenic	PAH-related disorder	2024-06-25	no assertion criteria provided	clinical testing	The PAH c.441+5G>T variant is predicted to interfere with splicing. This variant, which lies near the junction of exon 4 and intron 4 and is predicted to disrupt splicing, has been reported as causative in either the homozygous or compound heterozygous state for phenylalanine hydroxylase deficiency (see for example Zekanowski et al. 1997. PubMed ID: 9429153; Bueno et al. 2013. PubMed ID: 23514811; Trunzo et al. 2013. PubMed ID: 24296287; Table S3 in Hillert et al. 2020. PubMed ID: 32668217). Other variants within the same splice site region (e.g., c.441+1G>A,c.441+2T>G, c.441+3G>C, c.441+6T>A) have been reported with a second PAH variant in individuals with phenylalanine hydroxylase deficiency (see for example Table S3 in Hillert et al. 2020. PubMed ID: 32668217). This variant is reported in 0.011% of alleles in individuals of Latino descent in gnomAD. This variant has been classified as pathogenic by the ClinGen PAH Variant Curation Expert Panel as well as multiple other submitters to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/92742/). Taken together, this variant is interpreted as pathogenic.