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NM_001384140.1(PCDH15):c.1900G>A (p.Val634Ile) AND not specified

Germline classification:
Benign (1 submission)
Last evaluated:
May 15, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000825082.4

Allele description [Variation Report for NM_001384140.1(PCDH15):c.1900G>A (p.Val634Ile)]

NM_001384140.1(PCDH15):c.1900G>A (p.Val634Ile)

Gene:
PCDH15:protocadherin related 15 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q21.1
Genomic location:
Preferred name:
NM_001384140.1(PCDH15):c.1900G>A (p.Val634Ile)
HGVS:
  • NC_000010.11:g.54132892C>T
  • NG_009191.3:g.1501291G>A
  • NM_001142763.2:c.1915G>A
  • NM_001142764.2:c.1900G>A
  • NM_001142765.2:c.1784+20208G>A
  • NM_001142766.2:c.1900G>A
  • NM_001142767.2:c.1789G>A
  • NM_001142768.2:c.1834G>A
  • NM_001142769.3:c.1936G>A
  • NM_001142770.3:c.1900G>A
  • NM_001142771.2:c.1915G>A
  • NM_001142772.2:c.1900G>A
  • NM_001142773.2:c.1834G>A
  • NM_001354404.2:c.1834G>A
  • NM_001354411.2:c.1921G>A
  • NM_001354420.2:c.1900G>A
  • NM_001354429.2:c.1900G>A
  • NM_001354430.2:c.1900G>A
  • NM_001384140.1:c.1900G>AMANE SELECT
  • NM_033056.4:c.1900G>A
  • NP_001136235.1:p.Val639Ile
  • NP_001136236.1:p.Val634Ile
  • NP_001136238.1:p.Val634Ile
  • NP_001136239.1:p.Val597Ile
  • NP_001136240.1:p.Val612Ile
  • NP_001136241.1:p.Val646Ile
  • NP_001136242.1:p.Val634Ile
  • NP_001136243.1:p.Val639Ile
  • NP_001136244.1:p.Val634Ile
  • NP_001136245.1:p.Val612Ile
  • NP_001341333.1:p.Val612Ile
  • NP_001341340.1:p.Val641Ile
  • NP_001341349.1:p.Val634Ile
  • NP_001341358.1:p.Val634Ile
  • NP_001341359.1:p.Val634Ile
  • NP_001371069.1:p.Val634Ile
  • NP_149045.3:p.Val634Ile
  • NC_000010.10:g.55892652C>T
  • NM_033056.3:c.1900G>A
  • p.Val634Ile
Protein change:
V597I
Links:
dbSNP: rs146199636
NCBI 1000 Genomes Browser:
rs146199636
Molecular consequence:
  • NM_001142765.2:c.1784+20208G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001142763.2:c.1915G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142764.2:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142766.2:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142767.2:c.1789G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142768.2:c.1834G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142769.3:c.1936G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142770.3:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142771.2:c.1915G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142772.2:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142773.2:c.1834G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354404.2:c.1834G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354411.2:c.1921G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354420.2:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354429.2:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354430.2:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384140.1:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033056.4:c.1900G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000966321Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Benign
(May 15, 2018) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided22not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000966321.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)

Description

p.Val634Ile in exon 15 of PCDH15: This variant is classified as benign due to a lack of conservation across species, including mammals. Of note, >40 mammals hav e an Isoleucine (Ile) at this position despite high nearby amino acid conservati on. In addition, computational prediction tools do not suggest a high likelihood of impact to the protein. It has been identified in 0.32% (97/30666) of South A sian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broad institute.org; dbSNP rs146199636). ACMG/AMP criteria applied: BS1, BP4_Strong.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided2not provided2not provided

Last Updated: Apr 15, 2024