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NM_001130438.3(SPTAN1):c.4580A>G (p.Asn1527Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000196941.6
Variation ID:
196941
Description:
single nucleotide variant
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NM_001130438.3(SPTAN1):c.4580A>G (p.Asn1527Ser)

Allele ID
194102
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.11
Genomic location
9: 128608962 (GRCh38) GRCh38 UCSC
9: 131371241 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.131371241A>G
NC_000009.12:g.128608962A>G
NM_001130438.3:c.4580A>G MANE Select NP_001123910.1:p.Asn1527Ser missense
... more HGVS
Protein change
N1527S, N1507S
Other names
p.N1527S:AAT>AGT
Canonical SPDI
NC_000009.12:128608961:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (G)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00044
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00108
The Genome Aggregation Database (gnomAD) 0.00038
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00046
The Genome Aggregation Database (gnomAD), exomes 0.00041
Links
ClinGen: CA244765
dbSNP: rs145038571
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Oct 31, 2017 RCV000189464.5
Likely benign 1 criteria provided, single submitter Jul 27, 2018 RCV000718427.1
Likely benign 1 criteria provided, single submitter Dec 2, 2020 RCV001086665.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 10, 2018 RCV000713515.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPTAN1 - - GRCh38
GRCh37
1236 1283

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Oct 31, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000243105.7
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Jul 10, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000844136.1
Submitted: (Aug 31, 2018)
Evidence details
Uncertain significance
(Jul 16, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000229775.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jul 27, 2018)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000849290.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Subpopulation frequency in support of benign classification
Likely benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000553149.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)

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
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SPTAN1 - - - -

Text-mined citations for rs145038571...

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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 May 16, 2021