NM_020631.6(PLEKHG5):c.2594A>G (p.Gln865Arg) AND Distal spinal muscular atrophy, autosomal recessive 4

Clinical significance:Benign (Last evaluated: Jan 12, 2018)
Review status:1 star out of maximum of 4 stars
criteria provided, single submitter

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Based on:: 1 submission [Details]
Record status:: current
Accession:: RCV000335865.2

Allele description [Variation Report for NM_020631.6(PLEKHG5):c.2594A>G (p.Gln865Arg)]

NM_020631.6(PLEKHG5):c.2594A>G (p.Gln865Arg)

Gene:

PLEKHG5:pleckstrin homology and RhoGEF domain containing G5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.31

Genomic location:

Preferred name:

NM_020631.6(PLEKHG5):c.2594A>G (p.Gln865Arg)

HGVS:

NC_000001.11:g.6468242T>C
NG_007978.1:g.56768A>G
NG_029910.1:g.2954A>G
NM_001042663.3:c.2705A>G
NM_001042664.1:c.2594A>G
NM_001042665.1:c.2594A>G
NM_001265592.2:c.2705A>G
NM_001265593.1:c.2801A>G
NM_001265594.2:c.2594A>G
NM_020631.6:c.2594A>GMANE SELECT
NM_198681.4:c.2594A>G
NP_001036128.2:p.Gln902Arg
NP_001036129.1:p.Gln865Arg
NP_001036130.1:p.Gln865Arg
NP_001252521.2:p.Gln902Arg
NP_001252522.1:p.Gln934Arg
NP_001252523.1:p.Gln865Arg
NP_065682.2:p.Gln865Arg
NP_941374.3:p.Gln865Arg
LRG_262:g.56768A>G
NC_000001.10:g.6528302T>C
NM_020631.4:c.2594A>G

Protein change:

Q865R

Links:

dbSNP: rs3007419

NCBI 1000 Genomes Browser:

rs3007419

Molecular consequence:

NM_001042663.3:c.2705A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001042664.1:c.2594A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001042665.1:c.2594A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001265592.2:c.2705A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001265593.1:c.2801A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001265594.2:c.2594A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_020631.6:c.2594A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198681.4:c.2594A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Distal spinal muscular atrophy, autosomal recessive 4 (DSMA4)
Identifiers:: MONDO: MONDO:0012608; MedGen: C1970211; Orphanet: 206580; OMIM: 611067

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000358724	Illumina Clinical Services Laboratory,Illumina	criteria provided, single submitter ICSL Variant Classification Criteria 13 December 2019	Benign (Jan 12, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000358724

Illumina Clinical Services Laboratory,Illumina

criteria provided, single submitter

ICSL Variant Classification Criteria 13 December 2019

Benign
(Jan 12, 2018)

germline

clinical testing

Citation Link

Summary from all submissions

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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

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000358724.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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: Nov 10, 2021

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