NM_000843.4(GRM6):c.38T>C (p.Val13Ala) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 23, 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:: RCV001910992.3

Allele description [Variation Report for NM_000843.4(GRM6):c.38T>C (p.Val13Ala)]

NM_000843.4(GRM6):c.38T>C (p.Val13Ala)

Gene:

GRM6:glutamate metabotropic receptor 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q35.3

Genomic location:

Preferred name:

NM_000843.4(GRM6):c.38T>C (p.Val13Ala)

HGVS:

NC_000005.10:g.178994907A>G
NG_008105.1:g.5217T>C
NM_000843.4:c.38T>CMANE SELECT
NP_000834.2:p.Val13Ala
LRG_1236t1:c.38T>C
LRG_1236:g.5217T>C
LRG_1236p1:p.Val13Ala
NC_000005.9:g.178421908A>G

Protein change:

V13A

Links:

dbSNP: rs1760747050

NCBI 1000 Genomes Browser:

rs1760747050

Molecular consequence:

NM_000843.4:c.38T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus ribonuclease, RNase A family, 13 (non-active) (Rnase13), mRNA
Mus musculus ribonuclease, RNase A family, 13 (non-active) (Rnase13), mRNA
gi|2211517547|ref|NM_001011687.3|

Nucleotide
ARHGAP12 [Prionailurus bengalensis]
ARHGAP12 [Prionailurus bengalensis]
Gene ID:122473218

Gene
CBTC649.fwd NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8932702 5', ...
CBTC649.fwd NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8932702 5', mRNA sequence
gi|126360581|gnl|dbEST|45046139|gb| 166.2|

Nucleotide
CBTC649.rev NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8932702 3', ...
CBTC649.rev NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8932702 3', mRNA sequence
gi|126268890|gnl|dbEST|45042717|gb| 165.1|

Nucleotide
CBTC7386.fwd NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8939665 5',...
CBTC7386.fwd NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8939665 5', mRNA sequence
gi|126270247|gnl|dbEST|45044074|gb| 522.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002164285	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 23, 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

SCV002164285

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 23, 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, SCV002164285.2

#	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, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 13 of the GRM6 protein (p.Val13Ala). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GRM6-related conditions. ClinVar contains an entry for this variant (Variation ID: 1391424). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GRM6 protein function. 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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