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NM_001195553.2(DCX):c.263C>G (p.Thr88Arg) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 28, 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:
RCV001922327.6

Allele description [Variation Report for NM_001195553.2(DCX):c.263C>G (p.Thr88Arg)]

NM_001195553.2(DCX):c.263C>G (p.Thr88Arg)

Gene:
DCX:doublecortin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq23
Genomic location:
Preferred name:
NM_001195553.2(DCX):c.263C>G (p.Thr88Arg)
HGVS:
  • NC_000023.11:g.111410136G>C
  • NG_011750.1:g.7043C>G
  • NM_000555.3:c.506C>G
  • NM_001195553.2:c.263C>GMANE SELECT
  • NM_001369370.1:c.263C>G
  • NM_001369371.1:c.263C>G
  • NM_001369372.1:c.263C>G
  • NM_001369373.1:c.263C>G
  • NM_001369374.1:c.263C>G
  • NM_178151.3:c.263C>G
  • NM_178152.3:c.263C>G
  • NM_178153.3:c.263C>G
  • NP_000546.2:p.Thr169Arg
  • NP_001182482.1:p.Thr88Arg
  • NP_001356299.1:p.Thr88Arg
  • NP_001356300.1:p.Thr88Arg
  • NP_001356301.1:p.Thr88Arg
  • NP_001356302.1:p.Thr88Arg
  • NP_001356303.1:p.Thr88Arg
  • NP_835364.1:p.Thr88Arg
  • NP_835365.1:p.Thr88Arg
  • NP_835366.1:p.Thr88Arg
  • NC_000023.10:g.110653364G>C
Protein change:
T169R
Links:
dbSNP: rs2147276286
NCBI 1000 Genomes Browser:
rs2147276286
Molecular consequence:
  • NM_000555.3:c.506C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195553.2:c.263C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369370.1:c.263C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369371.1:c.263C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369372.1:c.263C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369373.1:c.263C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369374.1:c.263C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_178151.3:c.263C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_178152.3:c.263C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_178153.3:c.263C>G - 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
SCV002151071Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 28, 2021) 		germlineclinical testing

PubMed (2)
[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

Magnetic resonance imaging and histological studies of corpus callosal and hippocampal abnormalities linked to doublecortin deficiency.

Kappeler C, Dhenain M, Phan Dinh Tuy F, Saillour Y, Marty S, Fallet-Bianco C, Souville I, Souil E, Pinard JM, Meyer G, Encha-Razavi F, Volk A, Beldjord C, Chelly J, Francis F.

J Comp Neurol. 2007 Jan 10;500(2):239-54.

PubMed [citation]
PMID:
17111359

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002151071.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

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.Thr88 amino acid residue in DCX. Other variant(s) that disrupt this residue have been observed in individuals with DCX-related conditions (PMID: 17111359), which suggests that this may be a clinically significant amino acid residue. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been observed in individual(s) with lissencephaly and subcortical band heterotopia (Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with arginine at codon 88 of the DCX protein (p.Thr88Arg). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and arginine.

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

Last Updated: Sep 29, 2024