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NM_152594.3(SPRED1):c.190C>T (p.Arg64Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Aug 4, 2020
Accession:
VCV000001813.3
Variation ID:
1813
Description:
single nucleotide variant
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NM_152594.3(SPRED1):c.190C>T (p.Arg64Ter)

Allele ID
16852
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38299530 (GRCh38) GRCh38 UCSC
15: 38591731 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.9:g.38591731C>T
NG_008980.1:g.51680C>T
NC_000015.10:g.38299530C>T
NM_152594.3:c.190C>T MANE Select NP_689807.1:p.Arg64Ter nonsense
Protein change
R64*
Other names
-
Canonical SPDI
NC_000015.10:38299529:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA251955
OMIM: 609291.0005
dbSNP: rs121434315
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Aug 4, 2020 RCV000001886.6
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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
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: SCV000782323.1
Submitted: (Dec 20, 2017)
Evidence details
Pathogenic
(Aug 04, 2020)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV000833323.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change creates a premature translational stop signal (p.Arg64*) in the SPRED1 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Jul 01, 2009)
no assertion criteria provided
Method: literature only
LEGIUS SYNDROME
Allele origin: germline
OMIM
Accession: SCV000022042.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)

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
SPRED1 germline mutations caused a neurofibromatosis type 1 overlapping phenotype. Pasmant E Journal of medical genetics 2009 PMID: 19366998
Germline loss-of-function mutations in SPRED1 cause a neurofibromatosis 1-like phenotype. Brems H Nature genetics 2007 PMID: 17704776

Text-mined citations for rs121434315...

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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