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NM_020631.6(PLEKHG5):c.307G>A (p.Val103Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000245660.14
Variation ID:
245660
Description:
single nucleotide variant
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NM_020631.6(PLEKHG5):c.307G>A (p.Val103Met)

Allele ID
244290
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p36.31
Genomic location
1: 6474583 (GRCh38) GRCh38 UCSC
1: 6534643 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.6534643C>T
LRG_262:g.50427G>A
NC_000001.11:g.6474583C>T
... more HGVS
Protein change
V103M, V172M, V140M
Other names
-
Canonical SPDI
NC_000001.11:6474582:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00260 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00179
The Genome Aggregation Database (gnomAD), exomes 0.00190
1000 Genomes Project 0.00260
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00269
Exome Aggregation Consortium (ExAC) 0.00195
Trans-Omics for Precision Medicine (TOPMed) 0.00229
Links
ClinGen: CA561882
dbSNP: rs141032388
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000313379.2
Uncertain significance 1 criteria provided, single submitter Apr 1, 2018 RCV000761631.5
Likely benign 1 criteria provided, single submitter Dec 3, 2020 RCV001083174.2
Uncertain significance 1 criteria provided, single submitter Jul 30, 2020 RCV001284857.2
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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
675 739

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Distal spinal muscular atrophy, autosomal recessive 4
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000358775.3
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)
Likely 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: SCV000646048.5
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jul 30, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001470950.1
Submitted: (Dec 11, 2020)
Evidence details
Comment:
The PLEKHG5 c.307G>A; p.Val103Met variant (rs141032388), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 245660). This … (more)
Uncertain significance
(Apr 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000891801.8
Submitted: (Jul 04, 2021)
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.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs141032388...

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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 11, 2021