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NM_152594.3(SPRED1):c.1225_1226delinsTT (p.Ala409Phe)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 23, 2020
Accession:
VCV000561784.6
Variation ID:
561784
Description:
2bp indel
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NM_152594.3(SPRED1):c.1225_1226delinsTT (p.Ala409Phe)

Allele ID
552852
Variant type
Indel
Variant length
2 bp
Cytogenetic location
15q14
Genomic location
15: 38351554-38351555 (GRCh38) GRCh38 UCSC
15: 38643755-38643756 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.38351554_38351555delinsTT
NC_000015.9:g.38643755_38643756delinsTT
NG_008980.1:g.103704_103705delinsTT
... more HGVS
Protein change
A409F
Other names
-
Canonical SPDI
NC_000015.10:38351553:GC:TT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs1566877075
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Apr 12, 2018 RCV000681186.1
Uncertain significance 1 criteria provided, single submitter Jun 26, 2020 RCV000818826.3
Likely benign 1 criteria provided, single submitter Nov 23, 2020 RCV001269110.1
Uncertain significance 1 no assertion criteria provided - RCV001261039.1
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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
412 434

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Apr 12, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000808644.1
Submitted: (Sep 14, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Nov 23, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001448352.1
Submitted: (Dec 02, 2020)
Evidence details
Comment:
Variant summary: SPRED1 c.1225_1226delinsTT (p.Ala409Phe) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Uncertain significance
(Jun 26, 2020)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV000959460.3
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change replaces alanine with phenylalanine at codon 409 of the SPRED1 protein (p.Ala409Phe). The alanine residue is moderately conserved and there is a … (more)
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
Noonan syndrome
Allele origin: unknown
Service de Génétique Moléculaire,Hôpital Robert Debré
Accession: SCV001438440.1
Submitted: (Mar 26, 2020)
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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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 rs1566877075...

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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 Oct 08, 2021