NM_013322.3(SNX10):c.194A>G (p.Gln65Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 22, 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:: RCV001874582.6

Allele description [Variation Report for NM_013322.3(SNX10):c.194A>G (p.Gln65Arg)]

NM_013322.3(SNX10):c.194A>G (p.Gln65Arg)

Gene:

SNX10:sorting nexin 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p15.2

Genomic location:

Preferred name:

NM_013322.3(SNX10):c.194A>G (p.Gln65Arg)

HGVS:

NC_000007.14:g.26364617A>G
NG_033902.1:g.77723A>G
NM_001199835.1:c.194A>G
NM_001199837.3:c.185A>G
NM_001199838.2:c.-41+115A>G
NM_001318198.1:c.272A>G
NM_001318199.3:c.194A>G
NM_001362753.1:c.272A>G
NM_001362754.1:c.272A>G
NM_013322.3:c.194A>GMANE SELECT
NP_001186764.1:p.Gln65Arg
NP_001186766.1:p.Gln62Arg
NP_001305127.1:p.Gln91Arg
NP_001305128.1:p.Gln65Arg
NP_001349682.1:p.Gln91Arg
NP_001349683.1:p.Gln91Arg
NP_037454.2:p.Gln65Arg
NC_000007.13:g.26404237A>G

Protein change:

Q62R

Links:

dbSNP: rs1476042289

NCBI 1000 Genomes Browser:

rs1476042289

Molecular consequence:

NM_001199838.2:c.-41+115A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001199835.1:c.194A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001199837.3:c.185A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318198.1:c.272A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318199.3:c.194A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001362753.1:c.272A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001362754.1:c.272A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_013322.3:c.194A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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AF4/FMR2 family member 1 isoform 1 [Mus musculus]
AF4/FMR2 family member 1 isoform 1 [Mus musculus]
gi|124248529|ref|NP_001074267.1|

Protein
Chain C, Protein tonB
Chain C, Protein tonB
gi|110590399|pdb|2GRX|C

Protein
3-Hydroxysteroid Dehydrogenases
3-Hydroxysteroid Dehydrogenases
Catalyze the oxidation of 3-hydroxysteroids to 3-ketosteroids.<br/>Year introduced: 1978

MeSH
Manikins
Manikins
Inanimate physical models which bear likeness to human beings and are used for various purposes in place of humans.<br/>Year introduced: 1991(1975)

MeSH
D-Xylulose Reductase
D-Xylulose Reductase
An enzyme that plays a role in the PENTOSES and GLUCURONATES interconversion pathway by catalyzing the oxidation of XYLITOL to D-xylulose. This enzyme has been found to be spe...<br/>Year introduced: 2006(1980)

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002131277	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 22, 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

SCV002131277

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 22, 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, SCV002131277.3

#	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. This variant has not been reported in the literature in individuals affected with SNX10-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamine with arginine at codon 65 of the SNX10 protein (p.Gln65Arg). The glutamine residue is moderately conserved and there is a small physicochemical difference between glutamine and arginine.

#	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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