NM_001384140.1(PCDH15):c.2138A>G (p.Asn713Ser) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 11, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000267122.7

Allele description [Variation Report for NM_001384140.1(PCDH15):c.2138A>G (p.Asn713Ser)]

NM_001384140.1(PCDH15):c.2138A>G (p.Asn713Ser)

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.2138A>G (p.Asn713Ser)

Other names:

NM_001384140.1(PCDH15):c.2138A>G; p.Asn713Ser

HGVS:

NC_000010.11:g.54066839T>C
NG_009191.3:g.1567344A>G
NM_001142763.2:c.2153A>G
NM_001142764.2:c.2138A>G
NM_001142765.2:c.1925A>G
NM_001142766.2:c.2138A>G
NM_001142767.2:c.2027A>G
NM_001142768.2:c.2072A>G
NM_001142769.3:c.2174A>G
NM_001142770.3:c.2138A>G
NM_001142771.2:c.2153A>G
NM_001142772.2:c.2138A>G
NM_001142773.2:c.2072A>G
NM_001354404.2:c.2072A>G
NM_001354411.2:c.2159A>G
NM_001354420.2:c.2138A>G
NM_001354429.2:c.2138A>G
NM_001354430.2:c.2138A>G
NM_001384140.1:c.2138A>GMANE SELECT
NM_033056.4:c.2138A>G
NP_001136235.1:p.Asn718Ser
NP_001136236.1:p.Asn713Ser
NP_001136237.1:p.Asn642Ser
NP_001136238.1:p.Asn713Ser
NP_001136239.1:p.Asn676Ser
NP_001136240.1:p.Asn691Ser
NP_001136241.1:p.Asn725Ser
NP_001136242.1:p.Asn713Ser
NP_001136243.1:p.Asn718Ser
NP_001136244.1:p.Asn713Ser
NP_001136245.1:p.Asn691Ser
NP_001341333.1:p.Asn691Ser
NP_001341340.1:p.Asn720Ser
NP_001341349.1:p.Asn713Ser
NP_001341358.1:p.Asn713Ser
NP_001341359.1:p.Asn713Ser
NP_001371069.1:p.Asn713Ser
NP_149045.3:p.Asn713Ser
NC_000010.10:g.55826599T>C
NC_000010.11:g.54066839T>C
NM_033056.3:c.2138A>G

Protein change:

N642S

Links:

dbSNP: rs190878515

NCBI 1000 Genomes Browser:

rs190878515

Molecular consequence:

NM_001142763.2:c.2153A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142764.2:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142765.2:c.1925A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142766.2:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142767.2:c.2027A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142768.2:c.2072A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142769.3:c.2174A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142770.3:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142771.2:c.2153A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142772.2:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142773.2:c.2072A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354404.2:c.2072A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354411.2:c.2159A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354420.2:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354429.2:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354430.2:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001384140.1:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_033056.4:c.2138A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/GBR/484...
Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/GBR/484861/2020, complete genome
gi|2180079990|gb|OM294022.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000340490	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Mar 16, 2016)	germline	clinical testing	Citation Link,
SCV003472901	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 11, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31054281, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000340490

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Mar 16, 2016)

germline

clinical testing

Citation Link,

SCV003472901

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 11, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genetic and Clinical Findings in a Large Cohort of Chinese Patients with Suspected Retinitis Pigmentosa.

Gao FJ, Li JK, Chen H, Hu FY, Zhang SH, Qi YH, Xu P, Wang DD, Wang LS, Chang Q, Zhang YJ, Liu W, Li W, Wang M, Chen F, Xu GZ, Wu JH.

Ophthalmology. 2019 Nov;126(11):1549-1556. doi: 10.1016/j.ophtha.2019.04.038. Epub 2019 May 1. Erratum in: Ophthalmology. 2020 Mar;127(3):434. doi: 10.1016/j.ophtha.2019.12.013.

PubMed [citation]

PMID:: 31054281

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 Eurofins Ntd Llc (ga), SCV000340490.3

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

#	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		1	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003472901.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 713 of the PCDH15 protein (p.Asn713Ser). This variant is present in population databases (rs190878515, gnomAD 0.006%). This missense change has been observed in individual(s) with clinical features of PCDH15-related conditions (PMID: 31054281). This variant is also known as c.2153A>G (p.Asn718Ser). ClinVar contains an entry for this variant (Variation ID: 286893). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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

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