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NM_024301.5(FKRP):c.235G>A (p.Val79Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 28, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000004229.7
Variation ID:
4229
Description:
single nucleotide variant
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NM_024301.5(FKRP):c.235G>A (p.Val79Met)

Allele ID
19268
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19q13.32
Genomic location
19: 46755685 (GRCh38) GRCh38 UCSC
19: 47258942 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q9H9S5:p.Val79Met
NC_000019.10:g.46755685G>A
NC_000019.9:g.47258942G>A
... more HGVS
Protein change
V79M
Other names
-
Canonical SPDI
NC_000019.10:46755684:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00439 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00159
1000 Genomes Project 0.00439
The Genome Aggregation Database (gnomAD) 0.00418
The Genome Aggregation Database (gnomAD), exomes 0.00103
Trans-Omics for Precision Medicine (TOPMed) 0.00467
Links
ClinGen: CA116716
UniProtKB: Q9H9S5#VAR_065055
OMIM: 606596.0012
dbSNP: rs104894683
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Feb 17, 2020 RCV000513718.4
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV001083979.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Oct 23, 2018 RCV000236146.8
Conflicting interpretations of pathogenicity 2 no assertion criteria provided Jan 10, 2020 RCV000004450.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FKRP - - GRCh38
GRCh37
535 565

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 03, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610960.1
Submitted: (Oct 05, 2017)
Evidence details
Benign
(Feb 17, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000293454.11
Submitted: (Sep 28, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 22995991, 18645206, 17113772, 14647208, 25898921)
Likely benign
(Dec 31, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000594778.1
Submitted: (Jul 05, 2017)
Evidence details
Benign
(Apr 12, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230415.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Oct 23, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001157673.1
Submitted: (Aug 05, 2019)
Evidence details
Comment:
The FKRP c.235G>A; p.Val79Met variant (rs104894683) is reported in several individuals affected with limb girdle muscular dystrophy (de Paula 2003), including three siblings that carried … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Walker-Warburg congenital muscular dystrophy
Allele origin: germline
Invitae
Accession: SCV000290695.7
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jan 10, 2020)
no assertion criteria provided
Method: clinical testing
Limb-girdle muscular dystrophy type 2I
Allele origin: germline
Natera, Inc.
Accession: SCV001460331.1
Submitted: (Dec 28, 2020)
Evidence details
Pathogenic
(Dec 01, 2003)
no assertion criteria provided
Method: literature only
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 5
Allele origin: germline
OMIM
Accession: SCV000024623.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

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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Title Author Journal Year Link
Asymptomatic carriers for homozygous novel mutations in the FKRP gene: the other end of the spectrum. de Paula F European journal of human genetics : EJHG 2003 PMID: 14647208
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=FKRP - - - -

Text-mined citations for rs104894683...

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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 02, 2021