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

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000235230.8
Variation ID:
235230
Description:
single nucleotide variant
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NM_020631.6(PLEKHG5):c.2594A>G (p.Gln865Arg)

Allele ID
236918
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p36.31
Genomic location
1: 6468242 (GRCh38) GRCh38 UCSC
1: 6528302 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_262:g.56768A>G
NC_000001.10:g.6528302T>C
NC_000001.11:g.6468242T>C
... more HGVS
Protein change
Q865R, Q934R, Q902R
Other names
-
Canonical SPDI
NC_000001.11:6468241:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.01158 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00370
1000 Genomes Project 0.01158
Trans-Omics for Precision Medicine (TOPMed) 0.01628
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01647
The Genome Aggregation Database (gnomAD) 0.01411
Trans-Omics for Precision Medicine (TOPMed) 0.01696
The Genome Aggregation Database (gnomAD) 0.01628
Exome Aggregation Consortium (ExAC) 0.00497
Links
ClinGen: CA561124
dbSNP: rs3007419
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Jul 31, 2018 RCV000312080.4
Benign 1 criteria provided, single submitter Nov 23, 2015 RCV000224958.5
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000335865.2
Benign 1 criteria provided, single submitter Dec 3, 2020 RCV001084429.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PLEKHG5 - - GRCh38
GRCh37
671 739

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Nov 23, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000280647.1
Submitted: (May 19, 2016)
Evidence details
Benign
(Mar 15, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000517061.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Jul 21, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000343457.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Distal spinal muscular atrophy, autosomal recessive 4
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000358724.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Distal spinal muscular atrophy, autosomal recessive 4
Charcot-Marie-Tooth disease, recessive intermediate c
Allele origin: germline
Invitae
Accession: SCV000646037.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 31, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000885979.2
Submitted: (Aug 05, 2019)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Text-mined citations for rs3007419...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021