NM_000285.4(PEPD):c.1363G>A (p.Val455Ile) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 14, 2021
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:: RCV001891290.5

Allele description [Variation Report for NM_000285.4(PEPD):c.1363G>A (p.Val455Ile)]

NM_000285.4(PEPD):c.1363G>A (p.Val455Ile)

Gene:

PEPD:peptidase D [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.11

Genomic location:

Preferred name:

NM_000285.4(PEPD):c.1363G>A (p.Val455Ile)

HGVS:

NC_000019.10:g.33387463C>T
NG_013358.2:g.139431G>A
NM_000285.3:c.1363G>A
NM_000285.4:c.1363G>AMANE SELECT
NM_001166056.2:c.1240G>A
NM_001166057.2:c.1171G>A
NP_000276.2:p.Val455Ile
NP_001159528.1:p.Val414Ile
NP_001159529.1:p.Val391Ile
NC_000019.9:g.33878369C>T

Protein change:

V391I

Links:

dbSNP: rs747974977

NCBI 1000 Genomes Browser:

rs747974977

Molecular consequence:

NM_000285.4:c.1363G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001166056.2:c.1240G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001166057.2:c.1171G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PIK3R1 phosphoinositide-3-kinase regulatory subunit 1 [Homo sapiens]
PIK3R1 phosphoinositide-3-kinase regulatory subunit 1 [Homo sapiens]
Gene ID:5295

Gene
NM_181523 AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002167065	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 14, 2021)	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

SCV002167065

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 14, 2021)

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, SCV002167065.2

#	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 valine with isoleucine at codon 455 of the PEPD protein (p.Val455Ile). The valine residue is moderately conserved and there is a small physicochemical difference between valine and isoleucine. This variant is present in population databases (rs747974977, ExAC 0.03%). This variant has not been reported in the literature in individuals affected with PEPD-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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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