Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_006939.4(SOS2):c.3952C>T (p.Pro1318Ser)

Help
Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Sep 13, 2021)
Last evaluated:
Dec 15, 2020
Accession:
VCV000475758.7
Variation ID:
475758
Description:
single nucleotide variant
Help

NM_006939.4(SOS2):c.3952C>T (p.Pro1318Ser)

Allele ID
463782
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
14q21.3
Genomic location
14: 50118391 (GRCh38) GRCh38 UCSC
14: 50585109 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000014.8:g.50585109G>A
NC_000014.9:g.50118391G>A
NG_051073.1:g.118303C>T
NM_006939.4:c.3952C>T MANE Select NP_008870.2:p.Pro1318Ser missense
Protein change
P1318S
Other names
-
Canonical SPDI
NC_000014.9:50118390:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00029
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00100
Trans-Omics for Precision Medicine (TOPMed) 0.00053
1000 Genomes Project 0.00080
Links
ClinGen: CA7176682
dbSNP: rs140995728
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Nov 9, 2020 RCV000555942.5
Likely benign 1 criteria provided, single submitter Mar 23, 2020 RCV001175493.1
Benign 1 criteria provided, single submitter Dec 15, 2020 RCV001644664.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SOS2 - - GRCh38
GRCh37
466 482

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Nov 09, 2020)
criteria provided, single submitter
Method: clinical testing
Noonan syndrome 9
Allele origin: germline
Invitae
Accession: SCV000656031.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Mar 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: SCV001339086.1
Submitted: (Apr 29, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: SOS2 c.3952C>T (p.Pro1318Ser) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging … (more)
Benign
(Dec 15, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001856913.1
Submitted: (Sep 13, 2021)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
Activating Mutations Affecting the Dbl Homology Domain of SOS2 Cause Noonan Syndrome. Cordeddu V Human mutation 2015 PMID: 26173643

Text-mined citations for rs140995728...

Help
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