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NM_018100.4(EFHC1):c.1612C>T (p.Arg538Ter)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Feb 1, 2019)
Last evaluated:
Dec 6, 2018
Accession:
VCV000205414.3
Variation ID:
205414
Description:
single nucleotide variant
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NM_018100.4(EFHC1):c.1612C>T (p.Arg538Ter)

Allele ID
202009
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6p12.2
Genomic location
6: 52479759 (GRCh38) GRCh38 UCSC
6: 52344557 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.12:g.52479759C>T
NC_000006.11:g.52344557C>T
NM_018100.4:c.1612C>T NP_060570.2:p.Arg538Ter nonsense
... more HGVS
Protein change
R538*
Other names
p.R538*:CGA>TGA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00003
Links
ClinGen: CA314462
dbSNP: rs149998588
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Jan 17, 2013 RCV000187372.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 6, 2018 RCV000679897.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EFHC1 - - GRCh38
GRCh37
226 240

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Sep 01, 2017)
criteria provided, single submitter
Method: clinical testing
Juvenile myoclonic epilepsy
(Autosomal dominant inheritance)
Allele origin: paternal
Baylor Genetics
Accession: SCV000807320.1
Submitted: (Oct 16, 2017)
Evidence details
Publications
PubMed (1)
Comment:
This nonsense mutation is categorized as deleterious according to ACMG guidelines (PMID:18414213). It was found once in our laboratory paternally inherited in a 15-year-old female ... (more)
Pathogenic
(Jan 17, 2013)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000240957.11
Submitted: (Jan 29, 2019)
Evidence details
Comment:
p.Arg538Stop (CGA>TGA): c.1612 C>T in exon 9 of the EFHC1 gene (NM_018100.3). The Arg538Stop nonsense mutation in the EFHC1 gene is predicted to cause loss ... (more)
Uncertain significance
(Dec 06, 2018)
criteria provided, single submitter
Method: clinical testing
Juvenile Myoclonic Epilepsy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000915175.1
Submitted: (Feb 01, 2019)
Evidence details
Comment:
The EFHC1 c.1612C>T (p.Arg538Ter) variant is a stop gained variant predicted to result in premature termination of the protein. The p.Arg538Ter variant has not been ... (more)

Citations for this variant

Title Author Journal Year Link
Molecular findings among patients referred for clinical whole-exome sequencing. Yang Y JAMA 2014 PMID: 25326635

Record last updated Jan 18, 2020