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NM_152594.3(SPRED1):c.304dup (p.Thr102fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Mar 28, 2019)
Last evaluated:
Oct 23, 2018
Accession:
VCV000536688.2
Variation ID:
536688
Description:
1bp duplication
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NM_152594.3(SPRED1):c.304dup (p.Thr102fs)

Allele ID
529256
Variant type
Duplication
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38322336-38322337 (GRCh38) GRCh38 UCSC
15: 38614537-38614538 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.38322337dup
NC_000015.9:g.38614538dup
NG_008980.1:g.74487dup
... more HGVS
Protein change
T102fs
Other names
-
Canonical SPDI
NC_000015.10:38322336:A:AA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00000
Links
ClinGen: CA489921765
dbSNP: rs1555391053
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Oct 23, 2018 RCV000645296.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
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
Pathogenic
(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: SCV000782324.1
Submitted: (Dec 20, 2017)
Evidence details
Pathogenic
(Oct 23, 2018)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV000767039.3
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change creates a premature translational stop signal (p.Thr102Asnfs*7) in the SPRED1 gene. It is expected to result in an absent or disrupted protein … (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
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
Legius syndrome in fourteen families. Denayer E Human mutation 2011 PMID: 21089071

Text-mined citations for rs1555391053...

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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