NM_138773.4(SLC25A46):c.19G>A (p.Asp7Asn) AND Neuropathy, hereditary motor and sensory, type 6B

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 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:: RCV001974011.4

Allele description [Variation Report for NM_138773.4(SLC25A46):c.19G>A (p.Asp7Asn)]

NM_138773.4(SLC25A46):c.19G>A (p.Asp7Asn)

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.19G>A (p.Asp7Asn)

HGVS:

NC_000005.10:g.110739138G>A
NG_051334.1:g.6003G>A
NM_001303249.3:c.19G>A
NM_001303250.3:c.10+891G>A
NM_138773.1:c.19G>A
NM_138773.4:c.19G>AMANE SELECT
NP_001290178.1:p.Asp7Asn
NP_620128.1:p.Asp7Asn
LRG_1091t1:c.19G>A
LRG_1091:g.6003G>A
LRG_1091p1:p.Asp7Asn
NC_000005.9:g.110074839G>A
NR_138151.2:n.132G>A

Protein change:

D7N

Links:

dbSNP: rs1295016936

NCBI 1000 Genomes Browser:

rs1295016936

Molecular consequence:

NM_001303250.3:c.10+891G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001303249.3:c.19G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_138773.4:c.19G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_138151.2:n.132G>A - 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

Clear Turn Off Turn On

Smc5-6 complex non-SMC MAGE family subunit Nse3 [Schizosaccharomyces pombe]
Smc5-6 complex non-SMC MAGE family subunit Nse3 [Schizosaccharomyces pombe]
gi|19075613|ref|NP_588113.1|

Protein
Caenorhabditis elegans Regulator of G-protein signaling 7 (eat-16), mRNA
Caenorhabditis elegans Regulator of G-protein signaling 7 (eat-16), mRNA
gi|1972232218|ref|NM_170911.6|

Nucleotide
Rattus norvegicus opioid related nociceptin receptor 1 (Oprl1), transcript varia...
Rattus norvegicus opioid related nociceptin receptor 1 (Oprl1), transcript variant 1, mRNA
gi|974515912|ref|NM_031569.4|

Nucleotide
TPR_REGION domain-containing protein [Caenorhabditis elegans]
TPR_REGION domain-containing protein [Caenorhabditis elegans]
gi|808358114|ref|NP_001294583.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002262819	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 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

SCV002262819

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 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, SCV002262819.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

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. 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. ClinVar contains an entry for this variant (Variation ID: 1478064). This variant has not been reported in the literature in individuals affected with SLC25A46-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.02%). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 7 of the SLC25A46 protein (p.Asp7Asn).

#	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

ClinVar

Relating variation to medicine