NM_001384140.1(PCDH15):c.1843C>T (p.Arg615Cys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 6, 2022
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:: RCV002573244.2

Allele description [Variation Report for NM_001384140.1(PCDH15):c.1843C>T (p.Arg615Cys)]

NM_001384140.1(PCDH15):c.1843C>T (p.Arg615Cys)

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.1843C>T (p.Arg615Cys)

HGVS:

NC_000010.11:g.54132949G>A
NG_009191.3:g.1501234C>T
NM_001142763.2:c.1858C>T
NM_001142764.2:c.1843C>T
NM_001142765.2:c.1784+20151C>T
NM_001142766.2:c.1843C>T
NM_001142767.2:c.1732C>T
NM_001142768.2:c.1777C>T
NM_001142769.3:c.1879C>T
NM_001142770.3:c.1843C>T
NM_001142771.2:c.1858C>T
NM_001142772.2:c.1843C>T
NM_001142773.2:c.1777C>T
NM_001354404.2:c.1777C>T
NM_001354411.2:c.1864C>T
NM_001354420.2:c.1843C>T
NM_001354429.2:c.1843C>T
NM_001354430.2:c.1843C>T
NM_001384140.1:c.1843C>TMANE SELECT
NM_033056.4:c.1843C>T
NP_001136235.1:p.Arg620Cys
NP_001136236.1:p.Arg615Cys
NP_001136238.1:p.Arg615Cys
NP_001136239.1:p.Arg578Cys
NP_001136240.1:p.Arg593Cys
NP_001136241.1:p.Arg627Cys
NP_001136242.1:p.Arg615Cys
NP_001136243.1:p.Arg620Cys
NP_001136244.1:p.Arg615Cys
NP_001136245.1:p.Arg593Cys
NP_001341333.1:p.Arg593Cys
NP_001341340.1:p.Arg622Cys
NP_001341349.1:p.Arg615Cys
NP_001341358.1:p.Arg615Cys
NP_001341359.1:p.Arg615Cys
NP_001371069.1:p.Arg615Cys
NP_149045.3:p.Arg615Cys
NC_000010.10:g.55892709G>A
NM_033056.3:c.1843C>T

Protein change:

R578C

Links:

dbSNP: rs139104747

NCBI 1000 Genomes Browser:

rs139104747

Molecular consequence:

NM_001142765.2:c.1784+20151C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001142763.2:c.1858C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142764.2:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142766.2:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142767.2:c.1732C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142768.2:c.1777C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142769.3:c.1879C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142770.3:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142771.2:c.1858C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142772.2:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142773.2:c.1777C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354404.2:c.1777C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354411.2:c.1864C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354420.2:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354429.2:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354430.2:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001384140.1:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_033056.4:c.1843C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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zinc finger protein 317 isoform 1 [Homo sapiens]
zinc finger protein 317 isoform 1 [Homo sapiens]
gi|190610008|ref|NP_065984.3|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003462865	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 6, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003462865

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 6, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003462865.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 615 of the PCDH15 protein (p.Arg615Cys). This variant is present in population databases (rs139104747, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PCDH15-related conditions. ClinVar contains an entry for this variant (Variation ID: 1209589). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine