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NM_152594.3(SPRED1):c.6C>A (p.Ser2Arg)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Feb 21, 2021)
Last evaluated:
Jul 7, 2020
Accession:
VCV000965391.3
Variation ID:
965391
Description:
single nucleotide variant
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NM_152594.3(SPRED1):c.6C>A (p.Ser2Arg)

Allele ID
957396
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38253191 (GRCh38) GRCh38 UCSC
15: 38545392 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.38253191C>A
NC_000015.9:g.38545392C>A
NG_008980.1:g.5341C>A
NM_152594.3:c.6C>A MANE Select NP_689807.1:p.Ser2Arg missense
Protein change
S2R
Other names
-
Canonical SPDI
NC_000015.10:38253190:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
Links
dbSNP: rs775693385
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jul 7, 2020 RCV001239829.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPRED1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
414 436

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 07, 2020)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV001412730.2
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change replaces serine with arginine at codon 2 of the SPRED1 protein (p.Ser2Arg). The serine residue is moderately conserved and there is a … (more)
Uncertain significance
(Jan 31, 2020)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: unknown
Baylor Genetics
Accession: SCV001523892.1
Submitted: (Feb 21, 2021)
Evidence details
Comment:
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

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 rs775693385...

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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 Nov 27, 2021