NM_015404.4(WHRN):c.1696G>C (p.Val566Leu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 15, 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:: RCV001213992.8

Allele description [Variation Report for NM_015404.4(WHRN):c.1696G>C (p.Val566Leu)]

NM_015404.4(WHRN):c.1696G>C (p.Val566Leu)

Gene:

WHRN:whirlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q32

Genomic location:

Preferred name:

NM_015404.4(WHRN):c.1696G>C (p.Val566Leu)

HGVS:

NC_000009.12:g.114407949C>G
NG_016700.1:g.102508G>C
NM_001083885.3:c.547G>C
NM_001173425.2:c.1696G>C
NM_001346890.1:c.643G>C
NM_015404.4:c.1696G>CMANE SELECT
NP_001077354.2:p.Val183Leu
NP_001166896.1:p.Val566Leu
NP_001333819.1:p.Val215Leu
NP_056219.3:p.Val566Leu
LRG_1094t1:c.1696G>C
LRG_1094:g.102508G>C
LRG_1094p1:p.Val566Leu
NC_000009.11:g.117170229C>G
NM_015404.3:c.1696G>C
c.1696G>C

Protein change:

V183L

Links:

dbSNP: rs189654215

NCBI 1000 Genomes Browser:

rs189654215

Molecular consequence:

NM_001083885.3:c.547G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001173425.2:c.1696G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001346890.1:c.643G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_015404.4:c.1696G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Nucleotide-diphospho-sugar transferase family protein [Arabidopsis thaliana]
Nucleotide-diphospho-sugar transferase family protein [Arabidopsis thaliana]
gi|1063696536|ref|NP_001322084.1|

Protein
Homo sapiens methionine adenosyltransferase 2 non-catalytic beta subunit (MAT2B)...
Homo sapiens methionine adenosyltransferase 2 non-catalytic beta subunit (MAT2B), transcript variant 2, mRNA
gi|422010900|ref|NM_182796.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001385655	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 15, 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

SCV001385655

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 15, 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, SCV001385655.5

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

Description

ClinVar contains an entry for this variant (Variation ID: 45662). This variant has not been reported in the literature in individuals affected with WHRN-related conditions. This variant is present in population databases (rs189654215, gnomAD 0.03%). This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 566 of the WHRN protein (p.Val566Leu). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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

ClinVar

Relating variation to medicine