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NM_001195553.2(DCX):c.139A>C (p.Ser47Arg) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 23, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001857334.4

Allele description [Variation Report for NM_001195553.2(DCX):c.139A>C (p.Ser47Arg)]

NM_001195553.2(DCX):c.139A>C (p.Ser47Arg)

Gene:
DCX:doublecortin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq23
Genomic location:
Preferred name:
NM_001195553.2(DCX):c.139A>C (p.Ser47Arg)
HGVS:
  • NC_000023.11:g.111410260T>G
  • NG_011750.1:g.6919A>C
  • NM_000555.3:c.382A>C
  • NM_001195553.2:c.139A>CMANE SELECT
  • NM_001369370.1:c.139A>C
  • NM_001369371.1:c.139A>C
  • NM_001369372.1:c.139A>C
  • NM_001369373.1:c.139A>C
  • NM_001369374.1:c.139A>C
  • NM_178151.3:c.139A>C
  • NM_178152.3:c.139A>C
  • NM_178153.3:c.139A>C
  • NP_000546.2:p.Ser128Arg
  • NP_001182482.1:p.Ser47Arg
  • NP_001356299.1:p.Ser47Arg
  • NP_001356300.1:p.Ser47Arg
  • NP_001356301.1:p.Ser47Arg
  • NP_001356302.1:p.Ser47Arg
  • NP_001356303.1:p.Ser47Arg
  • NP_835364.1:p.Ser47Arg
  • NP_835365.1:p.Ser47Arg
  • NP_835366.1:p.Ser47Arg
  • NC_000023.10:g.110653488T>G
  • O43602:p.Ser47Arg
Protein change:
S128R; SER47ARG
Links:
UniProtKB: O43602#VAR_007820; OMIM: 300121.0007; dbSNP: rs104894783
NCBI 1000 Genomes Browser:
rs104894783
Molecular consequence:
  • NM_000555.3:c.382A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195553.2:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369370.1:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369371.1:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369372.1:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369373.1:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369374.1:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_178151.3:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_178152.3:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_178153.3:c.139A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002256642Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 23, 2021) 		germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Doublecortin mutations cluster in evolutionarily conserved functional domains.

Sapir T, Horesh D, Caspi M, Atlas R, Burgess HA, Wolf SG, Francis F, Chelly J, Elbaum M, Pietrokovski S, Reiner O.

Hum Mol Genet. 2000 Mar 22;9(5):703-12. Erratum in: Hum Mol Genet 2000 May 22;9(9):1461.

PubMed [citation]
PMID:
10749977

DCX in PC12 cells: CREB-mediated transcription and neurite outgrowth.

Shmueli O, Gdalyahu A, Sorokina K, Nevo E, Avivi A, Reiner O.

Hum Mol Genet. 2001 May 1;10(10):1061-70.

PubMed [citation]
PMID:
11331616
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002256642.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C15"). ClinVar contains an entry for this variant (Variation ID: 11603). This missense change has been observed in individual(s) with lissencephaly and subcortical band heterotopia (PMID: 9489700). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 47 of the DCX protein (p.Ser47Arg). Experimental studies have shown that this missense change affects DCX function (PMID: 10749977, 11331616, 22857951). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant disrupts the p.Ser47 amino acid residue in DCX. Other variant(s) that disrupt this residue have been observed in individuals with DCX-related conditions (PMID: 9489700, 23365099), which suggests that this may be a clinically significant amino acid residue.

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

Last Updated: Sep 29, 2024