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NM_152594.3(SPRED1):c.926T>C (p.Val309Ala)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 30, 2021)
Last evaluated:
Apr 15, 2021
Accession:
VCV000178134.8
Variation ID:
178134
Description:
single nucleotide variant
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NM_152594.3(SPRED1):c.926T>C (p.Val309Ala)

Allele ID
176103
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38351255 (GRCh38) GRCh38 UCSC
15: 38643456 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.38351255T>C
NC_000015.9:g.38643456T>C
NG_008980.1:g.103405T>C
NM_152594.3:c.926T>C MANE Select NP_689807.1:p.Val309Ala missense
Protein change
V309A
Other names
-
Canonical SPDI
NC_000015.10:38351254:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00048
Trans-Omics for Precision Medicine (TOPMed) 0.00184
Exome Aggregation Consortium (ExAC) 0.00067
The Genome Aggregation Database (gnomAD) 0.00153
Trans-Omics for Precision Medicine (TOPMed) 0.00194
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00223
1000 Genomes Project 0.00200
The Genome Aggregation Database (gnomAD) 0.00204
Links
ClinGen: CA181530
dbSNP: rs114636635
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Apr 15, 2021 RCV000586323.4
Likely benign 1 criteria provided, single submitter Mar 19, 2012 RCV000154849.3
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Oct 27, 2020 RCV000456632.10
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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
413 435

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Mar 19, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000204531.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Val309Ala in Exon 07 of SPRED1: This variant is not expected to have clinical significance because it has been identified in 0.6% (21/3738) of African … (more)
Benign
(Apr 17, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000699951.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: The SPRED1 c.926T>C (p.Val309Ala) variant involves the alteration of a conserved nucleotide and is predicted to be benign by 3/5 in silico tools. … (more)
Uncertain significance
(Nov 01, 2016)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Center for Human Genetics, Inc,Center for Human Genetics, Inc
Accession: SCV000782327.1
Submitted: (Dec 20, 2017)
Evidence details
Benign
(Oct 15, 2017)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001274827.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (3)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Oct 27, 2020)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV000560562.6
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 15, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000730787.2
Submitted: (Sep 30, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 21548021, 22753041)
Uncertain significance
(Dec 08, 2014)
no assertion criteria provided
Method: clinical testing
Legius syndrome
Allele origin: germline
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital
Accession: SCV000692375.1
Submitted: (Jan 31, 2018)
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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Title Author Journal Year Link
Legius syndrome, an Update. Molecular pathology of mutations in SPRED1. Brems H The Keio journal of medicine 2013 PMID: 24334617
Review and update of SPRED1 mutations causing Legius syndrome. Brems H Human mutation 2012 PMID: 22753041
Identification of SPRED1 deletions using RT-PCR, multiplex ligation-dependent probe amplification and quantitative PCR. Spencer E American journal of medical genetics. Part A 2011 PMID: 21548021

Text-mined citations for rs114636635...

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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