NM_001136193.2(FASTKD2):c.527C>T (p.Ala176Val) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 19, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001559445.7

Allele description [Variation Report for NM_001136193.2(FASTKD2):c.527C>T (p.Ala176Val)]

NM_001136193.2(FASTKD2):c.527C>T (p.Ala176Val)

Gene:

FASTKD2:FAST kinase domains 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q33.3

Genomic location:

Preferred name:

NM_001136193.2(FASTKD2):c.527C>T (p.Ala176Val)

HGVS:

NC_000002.12:g.206767220C>T
NG_008984.1:g.6833C>T
NM_001136193.2:c.527C>TMANE SELECT
NM_001136194.2:c.527C>T
NM_014929.4:c.527C>T
NP_001129665.1:p.Ala176Val
NP_001129666.1:p.Ala176Val
NP_055744.2:p.Ala176Val
NP_055744.2:p.Ala176Val
NC_000002.11:g.207631944C>T
NM_014929.3:c.527C>T

Protein change:

A176V

Links:

dbSNP: rs367909050

NCBI 1000 Genomes Browser:

rs367909050

Molecular consequence:

NM_001136193.2:c.527C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136194.2:c.527C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_014929.4:c.527C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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nucleosome assembly protein 1-like 4 isoform 2 [Homo sapiens]
nucleosome assembly protein 1-like 4 isoform 2 [Homo sapiens]
gi|1609043186|ref|NP_001356315.1|

Protein
NADH dehydrogenase subunit 6 (mitochondrion) [Gonodactylaceus falcatus]
NADH dehydrogenase subunit 6 (mitochondrion) [Gonodactylaceus falcatus]
gi|2806885854|gb|XHB32451.1|

Protein
Invertebrate sample from Thyasira tokunagai
Invertebrate sample from Thyasira tokunagai

biosample
TBLA0F02210 [Tetrapisispora blattae CBS 6284]
TBLA0F02210 [Tetrapisispora blattae CBS 6284]
Gene ID:14496872

Gene
Intestinal Secretions
Intestinal Secretions
Fluids originating from the epithelial lining of the intestines, adjoining exocrine glands and from organs such as the liver, which empty into the cavity of the intestines....<br/>

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001781671	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Nov 22, 2019)	germline	clinical testing	Citation Link,
SCV002189206	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 19, 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

SCV001781671

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Nov 22, 2019)

germline

clinical testing

Citation Link,

SCV002189206

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 19, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 GeneDx, SCV001781671.1

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002189206.2

#	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 alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 176 of the FASTKD2 protein (p.Ala176Val). This variant is present in population databases (rs367909050, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with FASTKD2-related conditions. ClinVar contains an entry for this variant (Variation ID: 333802). 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 expected to disrupt FASTKD2 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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