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NM_133433.4(NIPBL):c.2294G>A (p.Arg765Lys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Mar 14, 2019)
Last evaluated:
Aug 3, 2018
Accession:
VCV000159051.2
Variation ID:
159051
Description:
single nucleotide variant
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NM_133433.4(NIPBL):c.2294G>A (p.Arg765Lys)

Allele ID
168354
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5p13.2
Genomic location
5: 36985474 (GRCh38) GRCh38 UCSC
5: 36985576 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.36985474G>A
NC_000005.9:g.36985576G>A
NM_015384.5:c.2294G>A NP_056199.2:p.Arg765Lys missense
... more HGVS
Protein change
R765K
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
1000 Genomes Project 0.00040
Exome Aggregation Consortium (ExAC) 0.00055
The Genome Aggregation Database (gnomAD) 0.00115
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
Trans-Omics for Precision Medicine (TOPMed) 0.00050
The Genome Aggregation Database (gnomAD), exomes 0.00052
Links
ClinGen: CA239387
dbSNP: rs185678374
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Apr 27, 2016 RCV000254129.2
Likely benign 2 criteria provided, multiple submitters, no conflicts Aug 3, 2018 RCV000513777.2
Uncertain significance 1 criteria provided, single submitter Feb 8, 2013 RCV000146540.1
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000376495.1
Benign 1 criteria provided, single submitter Jul 1, 2016 RCV000719873.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NIPBL Sufficient evidence for dosage pathogenicity Little evidence for dosage pathogenicity GRCh38
GRCh37
644 721

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Feb 08, 2013)
criteria provided, single submitter
Method: clinical testing
Cornelia de Lange syndrome 1
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000193835.1
Submitted: (Sep 11, 2014)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000315679.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Apr 27, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000225093.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/em...
Benign
(Jul 01, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000850744.2
Submitted: (Jul 30, 2018)
Evidence details
Comment:
Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence ... (more)
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Cornelia de Lange Syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000457277.2
Submitted: (Oct 18, 2016)
Evidence details
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: SCV000610860.1
Submitted: (Oct 05, 2017)
Evidence details
Likely benign
(Aug 03, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001016592.1
Submitted: (Mar 14, 2019)
Evidence details

Citations for this variant

Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NIPBL - - - -

Record last updated Jan 11, 2020