NM_015404.4(WHRN):c.1075G>A (p.Val359Ile) AND not specified

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jul 15, 2016
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:: RCV000330120.8

Allele description [Variation Report for NM_015404.4(WHRN):c.1075G>A (p.Val359Ile)]

NM_015404.4(WHRN):c.1075G>A (p.Val359Ile)

Gene:

WHRN:whirlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q32

Genomic location:

Preferred name:

NM_015404.4(WHRN):c.1075G>A (p.Val359Ile)

HGVS:

NC_000009.12:g.114426302C>T
NG_016700.1:g.84155G>A
NM_001083885.3:c.-75G>A
NM_001173425.2:c.1075G>A
NM_015404.4:c.1075G>AMANE SELECT
NP_001166896.1:p.Val359Ile
NP_056219.3:p.Val359Ile
LRG_1094t1:c.1075G>A
LRG_1094:g.84155G>A
LRG_1094p1:p.Val359Ile
NC_000009.11:g.117188582C>T
NM_015404.2:c.1075G>A
NM_015404.3:c.1075G>A

Protein change:

V359I

Links:

dbSNP: rs147500559

NCBI 1000 Genomes Browser:

rs147500559

Molecular consequence:

NM_001083885.3:c.-75G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001173425.2:c.1075G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015404.4:c.1075G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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Homo sapiens axin 1 (AXIN1), RefSeqGene on chromosome 16
Homo sapiens axin 1 (AXIN1), RefSeqGene on chromosome 16
gi|238814318|ref|NG_012267.1|

Nucleotide
ATMND1 Mnd1 family protein [Arabidopsis thaliana]
ATMND1 Mnd1 family protein [Arabidopsis thaliana]
Gene ID:829038

Gene
Mitochondrial substrate carrier family protein [Arabidopsis thaliana]
Mitochondrial substrate carrier family protein [Arabidopsis thaliana]
Gene ID:838018

Gene
uncharacterized protein [Arabidopsis thaliana]
uncharacterized protein [Arabidopsis thaliana]
Gene ID:829884

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000343174	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Likely benign (Jul 15, 2016)	germline	clinical testing	Citation Link,
SCV000711013	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Jun 21, 2016)	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

SCV000343174

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Likely benign
(Jul 15, 2016)

germline

clinical testing

Citation Link,

SCV000711013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(Jun 21, 2016)

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	not provided	1	1	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Eurofins Ntd Llc (ga), SCV000343174.4

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

#	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		1	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000711013.2

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

Description

p.Val359Ile in exon 4 of DFNB31: This variant is not expected to have clinical s ignificance due to a lack of conservation across species, including mammals. Of note, three mammals (cow, hedgehog, and platypus) have an isoleucine (Ile) at th is position despite high nearby amino acid conservation. In addition, computatio nal prediction tools do not suggest a high likelihood of impact to the protein. This variant has been identified in 0.2% (21/10300) of African chromosomes by th e Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs14 7500559).

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

Last Updated: Oct 13, 2024

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