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NM_020631.6(PLEKHG5):c.509C>T (p.Pro170Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Aug 19, 2021)
Last evaluated:
Nov 24, 2020
Accession:
VCV000468916.7
Variation ID:
468916
Description:
single nucleotide variant
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NM_020631.6(PLEKHG5):c.509C>T (p.Pro170Leu)

Allele ID
448411
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p36.31
Genomic location
1: 6474095 (GRCh38) GRCh38 UCSC
1: 6534155 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.11:g.6474095G>A
NG_007978.1:g.50915C>T
NM_001042663.3:c.620C>T NP_001036128.2:p.Pro207Leu missense
... more HGVS
Protein change
P170L, P239L, P207L
Other names
-
Canonical SPDI
NC_000001.11:6474094:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00339 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00058
Trans-Omics for Precision Medicine (TOPMed) 0.00136
1000 Genomes Project 0.00339
The Genome Aggregation Database (gnomAD) 0.00105
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00131
Links
ClinGen: CA561829
dbSNP: rs59117380
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 Nov 24, 2020 RCV000555958.4
Uncertain significance 1 criteria provided, single submitter Aug 14, 2020 RCV001568993.3
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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
(Nov 24, 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: SCV000646055.4
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Aug 14, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001792960.1
Submitted: (Aug 19, 2021)
Evidence details
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to … (more)

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 rs59117380...

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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 Oct 30, 2021