NM_012431.3(SEMA3E):c.2048A>G (p.Asn683Ser) AND CHARGE association

Clinical significance:Uncertain significance (Last evaluated: Jun 28, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000529199.1

Allele description [Variation Report for NM_012431.3(SEMA3E):c.2048A>G (p.Asn683Ser)]

NM_012431.3(SEMA3E):c.2048A>G (p.Asn683Ser)

Gene:
SEMA3E:semaphorin 3E [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.11
Genomic location:
Preferred name:
NM_012431.3(SEMA3E):c.2048A>G (p.Asn683Ser)
HGVS:
  • NC_000007.14:g.83367866T>C
  • NG_021242.2:g.286298A>G
  • NM_001178129.2:c.1868A>G
  • NM_012431.3:c.2048A>GMANE SELECT
  • NP_001171600.1:p.Asn623Ser
  • NP_036563.1:p.Asn683Ser
  • LRG_1287t1:c.2048A>G
  • LRG_1287:g.286298A>G
  • LRG_1287p1:p.Asn683Ser
  • NC_000007.13:g.82997182T>C
  • NM_012431.2:c.2048A>G
Protein change:
N623S
Links:
dbSNP: rs144370841
NCBI 1000 Genomes Browser:
rs144370841
Molecular consequence:
  • NM_001178129.2:c.1868A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_012431.3:c.2048A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
CHARGE association (CHARGE)
Synonyms:
CHARGE ASSOCIATION--COLOBOMA, HEART ANOMALY, CHOANAL ATRESIA, RETARDATION, GENITAL AND EAR ANOMALIES; CHARGE syndrome; Coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008965; MedGen: C0265354; Orphanet: 138; OMIM: 214800

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000631232Invitaecriteria provided, single submitter
Uncertain significance
(Jun 28, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000631232.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces asparagine with serine at codon 683 of the SEMA3E protein (p.Asn683Ser). The asparagine residue is weakly conserved and there is a small physicochemical difference between asparagine and serine. This variant is present in population databases (rs144370841, ExAC 0.1%). This variant has not been reported in the literature in individuals with a SEMA3E-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, this variant has uncertain impact on SEMA3E function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 6, 2021

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