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NM_006306.4(SMC1A):c.1495C>T (p.Arg499Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 9, 2020
Accession:
VCV000489224.4
Variation ID:
489224
Description:
single nucleotide variant
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NM_006306.4(SMC1A):c.1495C>T (p.Arg499Ter)

Allele ID
482261
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xp11.22
Genomic location
X: 53409112 (GRCh38) GRCh38 UCSC
X: 53436043 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_773:g.18559C>T
LRG_773t1:c.1429C>T LRG_773p1:p.Arg477Ter
LRG_773t2:c.1495C>T LRG_773p2:p.Arg499Ter
... more HGVS
Protein change
R477*, R499*
Other names
-
Canonical SPDI
NC_000023.11:53409111:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA413255441
dbSNP: rs1556890135
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Nov 30, 2017 RCV000578696.1
Pathogenic 1 criteria provided, single submitter Oct 9, 2020 RCV001387822.1
SMC1A-related cohesinopathy
Pathogenic 1 criteria provided, single submitter May 1, 2019 RCV001270901.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SMC1A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
453 610

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Nov 30, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000681217.2
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R499X nonsense variant in the SMC1A gene is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. … (more)
Pathogenic
(May 01, 2019)
criteria provided, single submitter
Method: clinical testing
SMC1A-related cohesinopathy
Allele origin: unknown
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001451682.1
Submitted: (Dec 14, 2020)
Evidence details
Comment:
The SMC1A c.1495C>T (p.Arg499Ter) variant is a stop-gained variant that is predicted to result in an absent or truncated protein. A literature search was performed … (more)
Pathogenic
(Oct 09, 2020)
criteria provided, single submitter
Method: clinical testing
Congenital muscular hypertrophy-cerebral syndrome
Allele origin: germline
Invitae
Accession: SCV001588541.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change creates a premature translational stop signal (p.Arg499*) in the SMC1A gene. It is expected to result in an absent or disrupted protein … (more)

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
Cohesin complex-associated holoprosencephaly. Kruszka P Brain : a journal of neurology 2019 PMID: 31334757
A novel nonsense <i>SMC1A</i> mutation in a patient with intractable epilepsy and cardiac malformation. Chinen Y Human genome variation 2019 PMID: 31098032
Phenotypes and genotypes in individuals with SMC1A variants. Huisman S American journal of medical genetics. Part A 2017 PMID: 28548707
Heterozygous truncation mutations of the SMC1A gene cause a severe early onset epilepsy with cluster seizures in females: Detailed phenotyping of 10 new cases. Symonds JD Epilepsia 2017 PMID: 28166369
Mutations in HECW2 are associated with intellectual disability and epilepsy. Halvardson J Journal of medical genetics 2016 PMID: 27334371
Novel SMC1A frameshift mutations in children with developmental delay and epilepsy. Goldstein JH European journal of medical genetics 2015 PMID: 26386245

Text-mined citations for rs1556890135...

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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 24, 2021