NM_000285.4(PEPD):c.1463C>G (p.Pro488Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 25, 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:: RCV002003284.3

Allele description [Variation Report for NM_000285.4(PEPD):c.1463C>G (p.Pro488Arg)]

NM_000285.4(PEPD):c.1463C>G (p.Pro488Arg)

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.1463C>G (p.Pro488Arg)

HGVS:

NC_000019.10:g.33387363G>C
NG_013358.2:g.139531C>G
NM_000285.3:c.1463C>G
NM_000285.4:c.1463C>GMANE SELECT
NM_001166056.2:c.1340C>G
NM_001166057.2:c.1271C>G
NP_000276.2:p.Pro488Arg
NP_001159528.1:p.Pro447Arg
NP_001159529.1:p.Pro424Arg
NC_000019.9:g.33878269G>C

Protein change:

P424R

Links:

dbSNP: rs200567073

NCBI 1000 Genomes Browser:

rs200567073

Molecular consequence:

NM_000285.4:c.1463C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001166056.2:c.1340C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001166057.2:c.1271C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens mRNA for xylosyltransferase II (XT-II gene)
Homo sapiens mRNA for xylosyltransferase II (XT-II gene)
gi|11322269|emb|AJ277442.1|

Nucleotide
Mus musculus strain BALB/cJ 4930503L19Rik isoform 13 transcript variant 22 mRNA,...
Mus musculus strain BALB/cJ 4930503L19Rik isoform 13 transcript variant 22 mRNA, complete cds
gi|313103269|gb|HQ439009.1|

Nucleotide
Mus musculus DNA segment, Chr 18, ERATO Doi 653, expressed, mRNA (cDNA clone MGC...
Mus musculus DNA segment, Chr 18, ERATO Doi 653, expressed, mRNA (cDNA clone MGC:163564 IMAGE:40130210), complete cds
gi|124298043|gb|BC131933.1|

Nucleotide
Mus musculus strain 129X1/SvJ 4930503L19Rik isoform 1 transcript variant 1 mRNA,...
Mus musculus strain 129X1/SvJ 4930503L19Rik isoform 1 transcript variant 1 mRNA, complete cds
gi|313103203|gb|HQ438976.1|

Nucleotide
Mus musculus strain SWR/J 4930503L19Rik isoform 4 transcript variant 7 mRNA, com...
Mus musculus strain SWR/J 4930503L19Rik isoform 4 transcript variant 7 mRNA, complete cds
gi|313103231|gb|HQ438990.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002270000	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 25, 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

SCV002270000

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 25, 2022)

germline

clinical testing

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

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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, SCV002270000.2

#	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 proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 488 of the PEPD protein (p.Pro488Arg). This variant is present in population databases (rs200567073, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with PEPD-related conditions. ClinVar contains an entry for this variant (Variation ID: 1483906). 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"). 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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