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_012431.3(SEMA3E):c.1855C>T (p.Arg619Cys)

Help
Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Nov 3, 2021)
Last evaluated:
Oct 15, 2020
Accession:
VCV000221681.4
Variation ID:
221681
Description:
single nucleotide variant
Help

NM_012431.3(SEMA3E):c.1855C>T (p.Arg619Cys)

Allele ID
223369
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.11
Genomic location
7: 83385314 (GRCh38) GRCh38 UCSC
7: 83014630 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.83014630G>A
LRG_1287:g.268850C>T
LRG_1287t1:c.1855C>T LRG_1287p1:p.Arg619Cys
... more HGVS
Protein change
R619C, R559C
Other names
-
Canonical SPDI
NC_000007.14:83385313:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00010
The Genome Aggregation Database (gnomAD) 0.00010
Trans-Omics for Precision Medicine (TOPMed) 0.00011
The Genome Aggregation Database (gnomAD), exomes 0.00008
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00031
Links
ClinGen: CA354827
OMIM: 608166.0002
dbSNP: rs143631464
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, single submitter Oct 15, 2020 RCV000207418.2
Uncertain significance 1 criteria provided, single submitter Aug 18, 2020 RCV000231032.3
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SEMA3E - - GRCh38
GRCh37
318 337

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Aug 18, 2020)
criteria provided, single submitter
Method: clinical testing
CHARGE association
Allele origin: germline
Invitae
Accession: SCV000289888.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces arginine with cysteine at codon 619 of the SEMA3E protein (p.Arg619Cys). The arginine residue is moderately conserved and there is a … (more)
Uncertain significance
(Oct 15, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV002005128.1
Submitted: (Nov 03, 2021)
Evidence details
Comment:
Observed in siblings with Kallman syndrome who were also heterozygous for a variant in the CHD7 gene and observed in a patient with CHARGE syndrome … (more)
Uncertain significance
(Feb 09, 2016)
no assertion criteria provided
Method: literature only
VARIANT OF UNKNOWN SIGNIFICANCE
Allele origin: germline
OMIM
Accession: SCV000262695.1
Submitted: (Feb 09, 2016)
Evidence details
Publications
PubMed (1)

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
Dysfunctional SEMA3E signaling underlies gonadotropin-releasing hormone neuron deficiency in Kallmann syndrome. Cariboni A The Journal of clinical investigation 2015 PMID: 25985275
SEMA3E mutation in a patient with CHARGE syndrome. Lalani SR Journal of medical genetics 2004 PMID: 15235037

Text-mined citations for rs143631464...

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 Nov 06, 2021