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NM_000214.3(JAG1):c.601C>T (p.Arg201Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Apr 1, 2020
Accession:
VCV000197123.8
Variation ID:
197123
Description:
single nucleotide variant
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NM_000214.3(JAG1):c.601C>T (p.Arg201Cys)

Allele ID
194284
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
20p12.2
Genomic location
20: 10658561 (GRCh38) GRCh38 UCSC
20: 10639209 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000020.10:g.10639209G>A
NC_000020.11:g.10658561G>A
NM_000214.3:c.601C>T MANE Select NP_000205.1:p.Arg201Cys missense
... more HGVS
Protein change
R201C
Other names
-
Canonical SPDI
NC_000020.11:10658560:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA245082
dbSNP: rs794727618
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Nov 5, 2018 RCV000697814.2
Uncertain significance 1 criteria provided, single submitter Mar 24, 2020 RCV001175471.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 1, 2020 RCV000178063.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
JAG1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
782 813

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 05, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230050.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Nov 05, 2018)
criteria provided, single submitter
Method: clinical testing
Alagille syndrome 1
Allele origin: germline
Invitae
Accession: SCV000826445.2
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces arginine with cysteine at codon 201 of the JAG1 protein (p.Arg201Cys). The arginine residue is highly conserved and there is a … (more)
Uncertain significance
(Mar 24, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001339050.1
Submitted: (Apr 29, 2020)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: JAG1 c.601C>T (p.Arg201Cys) results in a non-conservative amino acid change located in the disulphide-rich Delta/Serrate/Lag-2 (DSL) protein domain (IPR001774 and Cordle_2008) of the … (more)
Likely pathogenic
(Apr 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001247224.5
Submitted: (Jul 04, 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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Title Author Journal Year Link
An Atypical Presentation of Alagille Syndrome. Wu KY Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society 2018 PMID: 29187043
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
A conserved face of the Jagged/Serrate DSL domain is involved in Notch trans-activation and cis-inhibition. Cordle J Nature structural & molecular biology 2008 PMID: 18660822
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=JAG1 - - - -

Text-mined citations for rs794727618...

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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 Jul 10, 2021