NM_138773.4(SLC25A46):c.93G>C (p.Arg31Ser) AND Neuropathy, hereditary motor and sensory, type 6B

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 20, 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:: RCV001931256.3

Allele description [Variation Report for NM_138773.4(SLC25A46):c.93G>C (p.Arg31Ser)]

NM_138773.4(SLC25A46):c.93G>C (p.Arg31Ser)

Gene:

SLC25A46:solute carrier family 25 member 46 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q22.1

Genomic location:

Preferred name:

NM_138773.4(SLC25A46):c.93G>C (p.Arg31Ser)

HGVS:

NC_000005.10:g.110739212G>C
NG_051334.1:g.6077G>C
NM_001303249.3:c.93G>C
NM_001303250.3:c.10+965G>C
NM_138773.4:c.93G>CMANE SELECT
NP_001290178.1:p.Arg31Ser
NP_620128.1:p.Arg31Ser
LRG_1091t1:c.93G>C
LRG_1091:g.6077G>C
LRG_1091p1:p.Arg31Ser
NC_000005.9:g.110074913G>C
NR_138151.2:n.206G>C

Protein change:

R31S

Links:

dbSNP: rs2150404149

NCBI 1000 Genomes Browser:

rs2150404149

Molecular consequence:

NM_001303250.3:c.10+965G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001303249.3:c.93G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_138773.4:c.93G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_138151.2:n.206G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Neuropathy, hereditary motor and sensory, type 6B (HMSN6B)
Synonyms:: HMSN VIB; CHARCOT-MARIE-TOOTH DISEASE, TYPE 6B; NEUROPATHY, HEREDITARY MOTOR AND SENSORY, TYPE VIB, WITH OPTIC ATROPHY; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0014671; MedGen: C4225302; OMIM: 616505

Recent activity

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Metagenome or environmental sample from viral metagenome
Metagenome or environmental sample from viral metagenome

biosample
olfactory receptor 52B6 [Homo sapiens]
olfactory receptor 52B6 [Homo sapiens]
gi|148229439|ref|NP_001005162.2|

Protein
L-histidine N(alpha)-methyltransferase [Mycobacterium tuberculosis]
L-histidine N(alpha)-methyltransferase [Mycobacterium tuberculosis]
gi|686050751|ref|WP_031735267.1|

Protein
zinc finger BED domain-containing protein 5 [Homo sapiens]
zinc finger BED domain-containing protein 5 [Homo sapiens]
gi|219521826|ref|NP_001137139.1|

Protein
Caenorhabditis elegans MABP domain-containing protein (B0001.5), mRNA
Caenorhabditis elegans MABP domain-containing protein (B0001.5), mRNA
gi|1972267404|ref|NM_069905.7|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002204881	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 20, 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

SCV002204881

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 20, 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, SCV002204881.2

#	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 arginine, which is basic and polar, with serine, which is neutral and polar, at codon 31 of the SLC25A46 protein (p.Arg31Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC25A46-related conditions. 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: "Deleterious"; PolyPhen-2: "Benign"; 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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