chr12-102843790-C-T

Variant names:

• chr12-102843790-C-T
• rs5030855
• NM_000277.3:c.1066-11G>A

Variant summary

Our verdict is Pathogenic. Variant got 8 ACMG points: 8P and 0B. PP4_Moderate PM3 PVS1_Strong

This summary comes from the ClinGen Evidence Repository: 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. (VCEPspecifications version 2; 12/06/24) LINK:https://erepo.genome.network/evrepo/ui/classification/CA251538/MONDO:0009861/006

• Frequency:
  • Genomes: 𝑓 0.00030 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00033 (0 hom.)
• Consequence: PAH NM_000277.3 intron
• Scores: Splicing: ADA: 0.9998
• Clinical Significance: Pathogenic reviewed by expert panel P:29 O:2
• Conservation: PhyloP100: 0.955

Genes affected

PAH (HGNC:8582): (phenylalanine hydroxylase) This gene encodes a member of the biopterin-dependent aromatic amino acid hydroxylase protein family. The encoded phenylalanine hydroxylase enzyme hydroxylates phenylalanine to tyrosine and is the rate-limiting step in phenylalanine catabolism. Deficiency of this enzyme activity results in the autosomal recessive disorder phenylketonuria. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 8 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAH	NM_000277.3	c.1066-11G>A		intron_variant	Intron 10 of 12	ENST00000553106.6	NP_000268.1
PAH	NM_001354304.2	c.1066-11G>A		intron_variant	Intron 11 of 13		NP_001341233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAH	ENST00000553106.6	c.1066-11G>A		intron_variant	Intron 10 of 12	1	NM_000277.3	ENSP00000448059.1

Frequencies

GnomAD3 genomes AF: 0.000302 AC: 46 AN: 152132 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000559

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000247 AC: 62 AN: 250674 Hom.: 0 AF XY: 0.000273 AC XY: 37 AN XY: 135518

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.0000993

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000980

Gnomad FIN exome AF: 0.0000468

Gnomad NFE exome AF: 0.000415

Gnomad OTH exome AF: 0.000818

GnomAD4 exome AF: 0.000327 AC: 478 AN: 1461036 Hom.: 0 Cov.: 33 AF XY: 0.000316 AC XY: 230 AN XY: 726862

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000580

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000400

Gnomad4 OTH exome AF: 0.000199

GnomAD4 genome AF: 0.000302 AC: 46 AN: 152250 Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21 AN XY: 74448

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000559

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000332 Hom.: 0

Bravo AF: 0.000314

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:29 Other:2

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:20 Other:1

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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 gene product 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. -

-

Centogene AG - the Rare Disease Company

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 03, 2017

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Sep 20, 2017

Natera, Inc.

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 30, 2024

ClinGen PAH Variant Curation Expert Panel

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: 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) -

Mar 08, 2022

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG classification criteria: PS3 supporting, PM3 very strong, PP1 supporting, PP3 supporting, PP4 -

Aug 09, 2022

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 01, 2019

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 01, 2023

Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 19, 2023

Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

pathogenic -

May 06, 2024

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 17, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Jun 30, 2022

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Feb 17, 2022

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 21, 2022

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PVS1, PS3, PP3 -

Jan 03, 2022

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

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Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM3_VeryStrong+PS3+PP4 -

Aug 15, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Mar 30, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 18, 2019

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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 -

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GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

not provided Pathogenic:7 Other:1

Feb 14, 2018

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Jul 19, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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) -

Dec 31, 2020

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Jul 30, 2024

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP3, PP4_moderate, PM2_moderate, PM3_strong, PS3 -

-

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PAH: PM3:Very Strong, PS3, PM2, PP4:Moderate, PP3 -

-

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Inborn genetic diseases Pathogenic:1

May 09, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Hyperphenylalaninemia Pathogenic:1

Oct 04, 2024

Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

PP4_Moderate, PS3, PM3_Strong -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Uncertain	25
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.98
SpliceAI score (max)		0.98		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.98		Position offset: -2
DS_AL_spliceai		0.61		Position offset: -11

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5030855; hg19: chr12-103237568;