NM_001034850.3(RETREG1):c.841A>G (p.Ser281Gly) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 22, 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:: RCV001868314.6

Allele description [Variation Report for NM_001034850.3(RETREG1):c.841A>G (p.Ser281Gly)]

NM_001034850.3(RETREG1):c.841A>G (p.Ser281Gly)

Gene:

RETREG1:reticulophagy regulator 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p15.1

Genomic location:

Preferred name:

NM_001034850.3(RETREG1):c.841A>G (p.Ser281Gly)

HGVS:

NC_000005.10:g.16478066T>C
NG_016644.2:g.143944A>G
NM_001034850.3:c.841A>GMANE SELECT
NM_019000.5:c.418A>G
NP_001030022.1:p.Ser281Gly
NP_001030022.1:p.Ser281Gly
NP_061873.2:p.Ser140Gly
LRG_363t1:c.841A>G
LRG_363:g.143944A>G
LRG_363p1:p.Ser281Gly
NC_000005.9:g.16478175T>C
NM_001034850.2:c.841A>G

Protein change:

S140G

Links:

dbSNP: rs1430719865

NCBI 1000 Genomes Browser:

rs1430719865

Molecular consequence:

NM_001034850.3:c.841A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_019000.5:c.418A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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SRP530628 (57)
SRA
Homo sapiens BAC clone RP13-582L3 from 4, complete sequence
Homo sapiens BAC clone RP13-582L3 from 4, complete sequence
gi|24080763|gb|AC116612.5||gnl|wugs 3-582L3

Nucleotide
PREDICTED: Homo sapiens glutamate rich 6B (ERICH6B), transcript variant X1, mRNA
PREDICTED: Homo sapiens glutamate rich 6B (ERICH6B), transcript variant X1, mRNA
gi|2217293701|ref|XM_011534965.3|

Nucleotide
PUTATIVE PSEUDOGENE: RecName: Full=Putative heat shock protein HSP 90-beta-3; Al...
PUTATIVE PSEUDOGENE: RecName: Full=Putative heat shock protein HSP 90-beta-3; AltName: Full=Heat shock protein 90-beta c; Short=Heat shock protein 90Bc
gi|74722492|sp|Q58FF7.1|H90B3_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002143514	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 22, 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

SCV002143514

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 22, 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, SCV002143514.3

#	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 serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 281 of the RETREG1 protein (p.Ser281Gly). This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with RETREG1-related conditions. ClinVar contains an entry for this variant (Variation ID: 579164). 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: "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

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