12-102839219-C-T

Variant names:

• chr12-102839219-C-T
• rs1592944816
• NM_000277.3:c.1316-1G>A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP4_Moderate PM2 PM3 PVS1_Strong

This summary comes from the ClinGen Evidence Repository: The c.1316-1G>A variant in PAH is a null variant (canonical +/- 1 or 2 splice sites) in a gene where LOF is a known mechanism of disease. It is predicted to result in skipping of coding exon 13, which is a key domain of the enzyme (PVS1_Strong). It is absent from ethnically diverse control databases, including gnomAD/ExAC, 1000 Genomes, and ESP (PM2). It has been previously reported in seven Ugyur probands (PMID:31355225): three homozygotes with mild PKU; one compound heterozygote with classic PKU in trans with the p.R413P variant (Pathogenic per ClinGen PAH working group); one compound heterozygote with classic PKU in trans with the p.R243Q variant (Pathogenic per ClinGen PAH working group); one compound heterozygote with mild PKU in trans with the p.A300S variant (Pathogenic per ClinGen PAH working group); and one compound heterozygote with mild PKU in trans with the p.E182K (Likely Pathogenic per ClinGen PAH working group) variant (PM3_VeryStrong). (In all cases, phase was confirmed by parental testing.) In all cases, BH4 deficiency was formally excluded by urinary pterin analysis (PP4_Moderate). It is reported pathogenic in Clinvar (ID 625286) by one lab, for PKU; no further information is given. LINK:https://erepo.genome.network/evrepo/ui/classification/CA386492907/MONDO:0009861/006

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: PAH NM_000277.3 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:2
• Conservation: PhyloP100: 4.32

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 10 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: 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.1316-1G>A		splice_acceptor_variant, intron_variant	Intron 12 of 12	ENST00000553106.6	NP_000268.1
PAH	NM_001354304.2	c.1316-1G>A		splice_acceptor_variant, intron_variant	Intron 13 of 13		NP_001341233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAH	ENST00000553106.6	c.1316-1G>A		splice_acceptor_variant, intron_variant	Intron 12 of 12	1	NM_000277.3	ENSP00000448059.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461494 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 727060

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:2

Jun 01, 2020

ClinGen PAH Variant Curation Expert Panel

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The c.1316-1G>A variant in PAH is a null variant (canonical +/- 1 or 2 splice sites) in a gene where LOF is a known mechanism of disease. It is predicted to result in skipping of coding exon 13, which is a key domain of the enzyme (PVS1_Strong). It is absent from ethnically diverse control databases, including gnomAD/ExAC, 1000 Genomes, and ESP (PM2). It has been previously reported in seven Ugyur probands (PMID: 31355225): three homozygotes with mild PKU; one compound heterozygote with classic PKU in trans with the p.R413P variant (Pathogenic per ClinGen PAH working group); one compound heterozygote with classic PKU in trans with the p.R243Q variant (Pathogenic per ClinGen PAH working group); one compound heterozygote with mild PKU in trans with the p.A300S variant (Pathogenic per ClinGen PAH working group); and one compound heterozygote with mild PKU in trans with the p.E182K (Likely Pathogenic per ClinGen PAH working group) variant (PM3_VeryStrong). (In all cases, phase was confirmed by parental testing.) In all cases, BH4 deficiency was formally excluded by urinary pterin analysis (PP4_Moderate). It is reported pathogenic in Clinvar (ID 625286) by one lab, for PKU; no further information is given. -

Mar 08, 2019

Center for Molecular Medicine, Children’s Hospital of Fudan University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.29
CADD	Pathogenic	31
DANN	Uncertain	0.99
Eigen	Pathogenic	0.94
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Uncertain	0.96	D
GERP RS		4.4

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.99		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1592944816; hg19: chr12-103232997;