NM_000277.3:c.1065+3A>C

Variant names:

• chr12-102844333-T-G
• rs62508689
• NM_000277.3:c.1065+3A>C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

This summary comes from the ClinGen Evidence Repository: (PAH):c.1065+3A>C is an intronic variant that is predicted to be splice altering in multiple lines of computational evidence. This variant was identified in a patient with an unspecified PKU/HPA phenotype. The variant was not specified to be heterozygous or homozygous (PMID 10394930). This variant is absent in population databases. In summary, this variant has insufficient evidence and is classified as uncertain significance for PAH. PAH-specific ACMG/AMP criteria applied: PM2 and PP3. LINK:https://erepo.genome.network/evrepo/ui/classification/CA229318/MONDO:0009861/006

• Frequency: Genomes: not found (cov: 32)
• Consequence: PAH NM_000277.3 splice_region, intron
• Scores: Splicing: ADA: 0.9995
• Clinical Significance: Uncertain significance reviewed by expert panel U:1 O:1
• Conservation: PhyloP100: 0.172

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 Uncertain_significance. Variant got 3 ACMG points.

• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: 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.1065+3A>C		splice_region_variant, intron_variant	Intron 10 of 12	ENST00000553106.6	NP_000268.1
PAH	NM_001354304.2	c.1065+3A>C		splice_region_variant, 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.1065+3A>C		splice_region_variant, intron_variant	Intron 10 of 12	1	NM_000277.3	ENSP00000448059.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Uncertain:1

Jul 30, 2020

ClinGen PAH Variant Curation Expert Panel

Significance: Uncertain significance

Review Status: reviewed by expert panel

Collection Method: curation

(PAH):c.1065+3A>C is an intronic variant that is predicted to be splice altering in multiple lines of computational evidence. This variant was identified in a patient with an unspecified PKU/HPA phenotype. The variant was not specified to be heterozygous or homozygous (PMID 10394930). This variant is absent in population databases. In summary, this variant has insufficient evidence and is classified as uncertain significance for PAH. PAH-specific ACMG/AMP criteria applied: PM2 and PP3. -

not provided Other:1

-

DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	19
DANN	Benign	0.91
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.95
SpliceAI score (max)		0.59		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.59		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs62508689; hg19: chr12-103238111;