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NM_152594.3(SPRED1):c.3G>A (p.Met1Ile)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
1 (Most recent: Jan 7, 2021)
Last evaluated:
Jan 14, 2019
Accession:
VCV000854050.2
Variation ID:
854050
Description:
single nucleotide variant
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NM_152594.3(SPRED1):c.3G>A (p.Met1Ile)

Allele ID
842240
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38253188 (GRCh38) GRCh38 UCSC
15: 38545389 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.9:g.38545389G>A
NG_008980.1:g.5338G>A
NM_152594.3:c.3G>A MANE Select NP_689807.1:p.Met1Ile missense
NC_000015.10:g.38253188G>A
Protein change
M1I
Other names
-
Canonical SPDI
NC_000015.10:38253187:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs1324903101
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Jan 14, 2019 RCV001059001.2
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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
Likely pathogenic
(Jan 14, 2019)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV001223604.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change affects the initiator methionine of the SPRED1 mRNA. The next in-frame methionine is located at codon 22. This variant is not present … (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
SPRED1 germline mutations caused a neurofibromatosis type 1 overlapping phenotype. Pasmant E Journal of medical genetics 2009 PMID: 19366998

Text-mined citations for rs1324903101...

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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