Submissions for variant NM_000277.3(PAH):c.1066-11G>A

gnomAD frequency: 0.00028  dbSNP: rs5030855

Total submissions: 31

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PAH Variant Curation Expert Panel	RCV000000638	SCV000852137	pathogenic	Phenylketonuria	2024-12-30	reviewed by expert panel	curation	The c.1066-11G>A variant in PAH occurs within intron 10. It is predicted to impact splicing of biologically-relevant-exon 11/13. This prediction is confirmed by RT-PCR analysis which showed an in-frame insertion of Gly, Leu, Gln between exon 10 and 11 (PMID: 1769645). Nonsense mediated decay does not occur, but the resulting protein has no enzymatic activity (altered region is critical to protein function, PVS1_strong). At least one patient with this variant displayed blood Phe > 30 mg/dl, which is highly specific for PAH deficiency (PMID: 8990013). BH4 deficiency was ruled out in 1 study (PMID: 23500595). This variant has been detected in at least 23 individuals with PAH deficiency. Of those individuals, 15 were compound heterozygous for the variant and a pathogenic variant [p.R252W, p.R243X, p.R261Q (4 patients), p.R270K, p.I65T (2 patients); 5.5 points] (PMID: 23500595; PMID: 8990013) (PM3_Very strong). The population allele frequency in gnomAD v4 is 0.0003248, which is higher than the PAH VCEP cutoff for PM2 (<0.0002). In summary, this variant meets criteria to be classified as pathogenic for PAH deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen PAH VCEP: PVS1_strong, PP4_Moderate, PM3_very-strong. (VCEP specifications version 2; 12/06/24)
Eurofins Ntd Llc (ga)	RCV000078500	SCV000110356	pathogenic	not provided	2018-02-14	criteria provided, single submitter	clinical testing
GeneDx	RCV000078500	SCV000239084	pathogenic	not provided	2024-07-19	criteria provided, single submitter	clinical testing	Associated with both a classical and a moderate PKU phenotype in patients who harbored a second variant in PAH (PMID: 12655546, 23500595); Activates a cryptic splice site in intron 10 and is expected to cause abnormal gene splicing (PMID: 1769645); Functional analysis revealed that c.1066-11 G>A is associated with 5% residual enzyme activity compared to wild type (PMID: 25596310); This variant is associated with the following publications: (PMID: 30747360, 28956315, 21147011, 19292873, 34828281, 25087612, 24296287, 22975760, 23348723, 23559577, 12655546, 1769645, 23500595, 26351554, 27469133, 26655635, 27922243, 24941924, 27121329, 28676969, 29499199, 31355225, 32533790, 31589614, 32905092, 33101986, 8188310, 34426522, 8445616, 7901929, 32778825, 29288420, 33375644, 34216551, 35405047, 37644014, 37421234, 36046396, 36646061, 37189584, 36537053, 17935162, 33465300, 32552793, 37924808, 25596310)
Fulgent Genetics, Fulgent Genetics	RCV000000638	SCV000611228	pathogenic	Phenylketonuria	2022-02-17	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000000638	SCV000629170	pathogenic	Phenylketonuria	2024-01-30	criteria provided, single submitter	clinical testing	This sequence change falls in intron 10 of the PAH gene. It does not directly change the encoded amino acid sequence of the PAH protein. RNA analysis indicates that this variant induces altered splicing and likely results in the gain of three amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs5030855, gnomAD 0.04%). This variant has been observed in individuals with phenylketonuria (PKU) (PMID: 1601425, 8990013, 22330942, 23430547, 23500595, 24296287, 25596310). It is commonly reported in individuals of European ancestry (PMID: 1601425, 8990013, 22330942, 23430547, 23500595, 24296287, 25596310). This variant is also known as p.Gln355_Tyr356insGlyLeuGln. ClinVar contains an entry for this variant (Variation ID: 607). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects PAH function (PMID: 1769645, 12655546, 25596310). Studies have shown that this variant results in the activation of a cryptic splice site in intron 10 (PMID: 1769645). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000000638	SCV000696424	pathogenic	Phenylketonuria	2017-01-03	criteria provided, single submitter	clinical testing	Variant summary: The PAH c.1066-11G>A variant is an intronic variant predicted to affect normal splicing by 4/5 splice prediction tools. This variant was found in 33/121034 control chromosomes at a frequency of 0.0002727, which does not exceed the estimated maximal expected allele frequency of a pathogenic PAH variant (0.0079057). This variant is a known pathogenic variant and is one of the most common pathogenic variants causing PKU. It activates a cryptic splice site and results in an in-frame insertion of 9 nucleotides between exon 10 and exon 11 of the processed mRNA. Normal amounts of liver PAH protein is present in homozygous patients, but no catalytic activity can be detected (Dworniczak_1991). This loss of enzyme activity is probably caused by conformational changes resulting from the insertion of three additional amino acids (Gly-Leu-Gln) between the normal sequences encoded by exon 10 and exon 11 (Dworniczak_1991). The patients who carried this variant in homozygous state were not responsive to BH4 challenge (Dobrowolski_2011). Several clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic.
Myriad Genetics, Inc.	RCV000000638	SCV001194159	pathogenic	Phenylketonuria	2019-10-18	criteria provided, single submitter	clinical testing	NM_000277.1(PAH):c.1066-11G>A is classified as pathogenic in the context of phenylalanine hydroxylase deficiency and is associated with the classic form of this disease. Sources cited for classification include the following: PMID 1769645 and 23500595. Classification of NM_000277.1(PAH):c.1066-11G>A is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.‚Äã
CeGaT Center for Human Genetics Tuebingen	RCV000078500	SCV001249171	pathogenic	not provided	2024-10-01	criteria provided, single submitter	clinical testing	PAH: PM3:Very Strong, PS3, PM2, PP4:Moderate, PP3
Centogene AG - the Rare Disease Company	RCV000000638	SCV001426525	pathogenic	Phenylketonuria		criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV000000638	SCV001440257	pathogenic	Phenylketonuria	2019-01-01	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000078500	SCV002047297	pathogenic	not provided	2020-12-31	criteria provided, single submitter	clinical testing	This variant is located 11 base pairs upstream of a canonical splice-acceptor site and interferes with normal PAH mRNA splicing. It has been reported to alter the splicing of exon 11 and cause the insertion of three amino acids that result in the protein having little to no residual activity (PMID: 1769645 (1991), BIOPKU (http://www.biopku.org/)). The variant is common especially in the Middle East and has been identified in families affected with classic PKU in the published literature (PMID: 23500595 (2013), 30389586 (2019), Gundorova et al. 2019 https://doi.org/10.1134/S1022795419080064). Therefore, the variant is classified as pathogenic.
3billion	RCV000000638	SCV002058573	pathogenic	Phenylketonuria	2022-01-03	criteria provided, single submitter	clinical testing	Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (, PS3_S). The variant has been reported multiple times as an established pathogenic/likely pathogenic variant (ClinVar ID: VCV000000607). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000248, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	RCV000000638	SCV002568298	pathogenic	Phenylketonuria	2022-04-21	criteria provided, single submitter	clinical testing	PVS1, PS3, PP3
Ambry Genetics	RCV002512611	SCV003682432	pathogenic	Inborn genetic diseases	2022-05-09	criteria provided, single submitter	clinical testing	The c.1066-11G>A intronic alteration consists of a G to A substitution 11 nucleotides before coding exon 11 in the PAH gene. Based on data from gnomAD, the A allele has an overall frequency of 0.02% (70/282062) total alleles studied. The highest observed frequency was 0.07% (5/7202) of Other alleles. This alteration has been detected in the homozygous state, and in trans with other PAH pathogenic mutations, in multiple individuals with phenylalanine hydroxylase deficiency (Tresbach, 2020; Carducci, 2020; Alsubaie, 2020; Couce, 2013; Trunzo, 2014). This nucleotide position is not well conserved in available vertebrate species. Functional assays confirm aberrant splicing that results in a 9nt in-frame insertion with a predicted protein effect of p.(Gln355_Tyr356insGlyLeuGln) (Dworniczak, 1991). Furthermore, PAH enzyme activity assays show low to absent enzyme activity in vitro and in a patient liver biopsy (Danecka, 2015; Pey, 2003; Dworniczak, 1991). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Based on the available evidence, this alteration is classified as pathogenic.
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	RCV000000638	SCV003807550	pathogenic	Phenylketonuria	2022-03-08	criteria provided, single submitter	clinical testing	ACMG classification criteria: PS3 supporting, PM3 very strong, PP1 supporting, PP3 supporting, PP4
Revvity Omics, Revvity	RCV000000638	SCV003826551	pathogenic	Phenylketonuria	2022-08-09	criteria provided, single submitter	clinical testing
Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences	RCV000000638	SCV004035235	pathogenic	Phenylketonuria	2023-09-19	criteria provided, single submitter	clinical testing	pathogenic
Baylor Genetics	RCV000000638	SCV004201314	pathogenic	Phenylketonuria	2024-03-30	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000078500	SCV004226633	pathogenic	not provided	2024-07-30	criteria provided, single submitter	clinical testing	PP3, PP4_moderate, PM2_moderate, PM3_strong, PS3
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	RCV000000638	SCV004804989	pathogenic	Phenylketonuria	2024-03-17	criteria provided, single submitter	research
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000000638	SCV004848681	pathogenic	Phenylketonuria	2022-06-30	criteria provided, single submitter	clinical testing	The c.1066-11G>A variant in PAH has been reported in >20 individuals with Phenylketonuria in the homozygous or compound heterozygous state and segregated with disease in multiple affected individuals (Desviat 1997 PMID: 8990013, Georgiou 2012 PMID: 22330942, Couce 2013 PMID: 23500595, Trunzo 2014 PMID: 24296287, Danecka 2015 PMID: 25596310). It has also been identified in 0.05% (38/68028) of European chromosomes by gnomAD v. 3 (http://gnomad.broadinstitute.org). This variant was classified as Pathogenic on Oct 01, 2018 by the ClinGen-approved PAH Variant Curation expert panel (Variation ID 607). Functional studies have shown that this variant activates a cryptic splice site and leads to an in-frame insertion of 3 amino acids to the transcript (Dworniczak 1991 PMID: 1769645). Additional in vitro functional studies have shown that this variant has no or little enzyme activity (Pey 2003 PMID: 12655546) and homozygotes had enzyme activity of 5% or less (Danecka 2015 PMID: 25596310). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive phenylketonuria. ACMG/AMP Criteria applied: PM3_VS, PS3, PP1_Strong.
Genomic Research Center, Shahid Beheshti University of Medical Sciences	RCV000000638	SCV005042983	pathogenic	Phenylketonuria	2024-05-06	criteria provided, single submitter	clinical testing
Juno Genomics, Hangzhou Juno Genomics, Inc	RCV000000638	SCV005418321	pathogenic	Phenylketonuria		criteria provided, single submitter	clinical testing	PM3_VeryStrong+PS3+PP4
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	RCV004798709	SCV005420351	pathogenic	Hyperphenylalaninemia	2024-10-04	criteria provided, single submitter	research	PP4_Moderate, PS3, PM3_Strong
OMIM	RCV000000638	SCV000020788	pathogenic	Phenylketonuria	2007-08-15	no assertion criteria provided	literature only
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	RCV000078500	SCV000119321	not provided	not provided		no assertion provided	not provided
GeneReviews	RCV000000638	SCV000324890	not provided	Phenylketonuria		no assertion provided	literature only
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000078500	SCV001930971	pathogenic	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000078500	SCV001959739	pathogenic	not provided		no assertion criteria provided	clinical testing
Natera, Inc.	RCV000000638	SCV002088635	pathogenic	Phenylketonuria	2017-09-20	no assertion criteria provided	clinical testing
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)	RCV000000638	SCV003927829	pathogenic	Phenylketonuria	2023-04-01	no assertion criteria provided	clinical testing