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NM_014140.4(SMARCAL1):c.1975C>T (p.Arg659Cys)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 9, 2020
Accession:
VCV000988238.2
Variation ID:
988238
Description:
single nucleotide variant
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NM_014140.4(SMARCAL1):c.1975C>T (p.Arg659Cys)

Allele ID
976065
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q35
Genomic location
2: 216450969 (GRCh38) GRCh38 UCSC
2: 217315692 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.217315692C>T
NC_000002.12:g.216450969C>T
NG_009771.1:g.43556C>T
... more HGVS
Protein change
R659C
Other names
-
Canonical SPDI
NC_000002.12:216450968:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
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 Oct 9, 2020 RCV001305151.1
Uncertain significance 1 no assertion criteria provided Oct 24, 2018 RCV001328268.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SMARCAL1 - - GRCh38
GRCh37
465 488

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 09, 2020)
criteria provided, single submitter
Method: clinical testing
Schimke immuno-osseous dysplasia
Allele origin: germline
Invitae
Accession: SCV001494473.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces arginine with cysteine at codon 659 of the SMARCAL1 protein (p.Arg659Cys). The arginine residue is highly conserved and there is a … (more)
Uncertain significance
(Oct 24, 2018)
no assertion criteria provided
Method: clinical testing
Atypical hemolytic uremic syndrome
Allele origin: unknown
Sydney Genome Diagnostics,Children's Hospital Westmead
Accession: SCV001449448.1
Submitted: (Sep 18, 2020)
Evidence details
Comment:
This patient is heterozygous for a variant of unknown clinical significance (VOUS), c.1975C>T p.(Arg659Cys), in exon 12 of the SMARCAL1 gene. To our knowledge, this … (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
Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders. Mallett AJ Kidney international 2017 PMID: 28844315

Record last updated Oct 08, 2021