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NM_000277.3(PAH):c.1315+2T>C

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Interpretation:
Likely pathogenic​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
4 (Most recent: Mar 6, 2020)
Last evaluated:
Dec 9, 2018
Accession:
VCV000102588.2
Variation ID:
102588
Description:
single nucleotide variant
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NM_000277.3(PAH):c.1315+2T>C

Allele ID
108324
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q23.2
Genomic location
12: 102840398 (GRCh38) GRCh38 UCSC
12: 103234176 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.103234176A>G
NC_000012.12:g.102840398A>G
NM_000277.3:c.1315+2T>C MANE Select splice donor
... more HGVS
Protein change
-
Other names
NM_000277.2(PAH):c.1315+2T>C
Canonical SPDI
NC_000012.12:102840397:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA229429
dbSNP: rs1799970
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 3 reviewed by expert panel Dec 9, 2018 RCV000169029.3
not provided 1 no assertion provided - RCV000088827.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PAH - - GRCh38
GRCh37
1103 1132

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Dec 09, 2018)
reviewed by expert panel
Method: curation
Phenylketonuria
(Autosomal recessive inheritance)
Allele origin: germline
ClinGen PAH Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV000886570.1
Submitted: (Feb 25, 2019)
Evidence details
Publications
PubMed (2)
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.1315+2T>C variant is at the 3' canonical splice site in the penultimate exon of PAH. It is absent form population databases and has been … (more)
Likely pathogenic
(Mar 18, 2014)
criteria provided, single submitter
Method: literature only
Phenylketonuria
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220178.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (2)
Pathogenic
(Jan 25, 2019)
criteria provided, single submitter
Method: clinical testing
Phenylketonuria
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001363424.1
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: PAH c.1315+2T>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE
Accession: SCV000119419.1
Submitted: (Mar 30, 2012)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Phenylalanine hydroxylase deficiency in south Italy: Genotype-phenotype correlations, identification of a novel mutant PAH allele and prediction of BH4 responsiveness. Trunzo R Clinica chimica acta; international journal of clinical chemistry 2015 PMID: 26210745
Phenylalanine hydroxylase deficiency in Mexico: genotype-phenotype correlations, BH4 responsiveness and evidence of a founder effect. Vela-Amieva M Clinical genetics 2015 PMID: 24941924
PAH gene mutations in the Sicilian population: association with minihaplotypes and expression analysis. Mirisola MG Molecular genetics and metabolism 2001 PMID: 11708866
Eight new mutations of the phenylalanine hydroxylase gene in Italian patients with hyperphenylalaninemia. Bosco P Human mutation 1998 PMID: 9521426
Identification of seven new mutations in the phenylalanine hydroxylase gene, associated with hyperphenylalaninemia in the Belgian population. Michiels L Human mutation 1998 PMID: 9452062
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/d9c83133-49d7-48ae-af5f-702bc7606dad - - - -

Text-mined citations for rs1799970...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 27, 2021