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NM_006579.3(EBP):c.511C>T (p.Arg171Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 21, 2021)
Last evaluated:
Dec 31, 2019
Accession:
VCV000158551.7
Variation ID:
158551
Description:
single nucleotide variant
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NM_006579.3(EBP):c.511C>T (p.Arg171Cys)

Allele ID
170133
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xp11.23
Genomic location
X: 48528275 (GRCh38) GRCh38 UCSC
X: 48386663 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.48386663C>T
NC_000023.11:g.48528275C>T
NG_007452.1:g.11500C>T
NM_006579.3:c.511C>T MANE Select NP_006570.1:p.Arg171Cys missense
Protein change
R171C
Other names
-
Canonical SPDI
NC_000023.11:48528274:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00026 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00073
Trans-Omics for Precision Medicine (TOPMed) 0.00077
1000 Genomes Project 0.00026
The Genome Aggregation Database (gnomAD) 0.00046
The Genome Aggregation Database (gnomAD), exomes 0.00064
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00066
Links
ClinGen: CA236348
dbSNP: rs141925556
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 5 criteria provided, multiple submitters, no conflicts Dec 31, 2019 RCV000171436.6
Likely benign 1 criteria provided, single submitter Jun 26, 2015 RCV000439113.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 28, 2019 RCV000145943.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EBP Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
92 260

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 26, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000517447.4
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
(Jun 17, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000885349.1
Submitted: (Oct 10, 2018)
Evidence details
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001024322.2
Submitted: (Jan 29, 2020)
Evidence details
Likely pathogenic
(Feb 08, 2013)
criteria provided, single submitter
Method: clinical testing
Chondrodysplasia punctata, X-linked dominant
(X-linked inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000193082.1
Submitted: (Sep 11, 2014)
Evidence details
Uncertain significance
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Chondrodysplasia punctata 2 X-linked dominant
Allele origin: unknown
Mendelics
Accession: SCV001141852.1
Submitted: (Oct 22, 2019)
Evidence details
Likely pathogenic
(-)
no assertion criteria provided
Method: research
Not provided
Allele origin: germline
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre
Accession: SCV000221634.1
Submitted: (Apr 14, 2015)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800541.1
Submitted: (Aug 19, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001965513.1
Submitted: (Sep 21, 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 rs141925556...

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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 07, 2021