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NM_003042.4(SLC6A1):c.1377C>A (p.Ser459Arg)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jul 4, 2021)
Last evaluated:
Jul 1, 2017
Accession:
VCV000421382.9
Variation ID:
421382
Description:
single nucleotide variant
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NM_003042.4(SLC6A1):c.1377C>A (p.Ser459Arg)

Allele ID
406083
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.3
Genomic location
3: 11031230 (GRCh38) GRCh38 UCSC
3: 11072916 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.11072916C>A
NC_000003.12:g.11031230C>A
NM_003042.4:c.1377C>A MANE Select NP_003033.3:p.Ser459Arg missense
... more HGVS
Protein change
S459R, S339R, S281R
Other names
-
Canonical SPDI
NC_000003.12:11031229:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA16617801
dbSNP: rs1064795099
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 - RCV000850413.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 1, 2017 RCV000487237.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SLC6A1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
284 425

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 03, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000570570.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The S459R variant in the SLC6A1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The … (more)
Likely pathogenic
(-)
criteria provided, single submitter
Method: research
Marfanoid habitus and intellectual disability
Allele origin: de novo
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV000992611.1
Submitted: (May 15, 2019)
Evidence details
Uncertain significance
(Jul 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001153794.6
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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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 rs1064795099...

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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