U.S. flag

An official website of the United States government

NM_001008537.3(NEXMIF):c.1789A>G (p.Thr597Ala) AND X-linked intellectual disability, Cantagrel type

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 17, 2017
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:
RCV000651331.1

Allele description

NM_001008537.3(NEXMIF):c.1789A>G (p.Thr597Ala)

Gene:
NEXMIF:neurite extension and migration factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq13.3
Genomic location:
Preferred name:
NM_001008537.3(NEXMIF):c.1789A>G (p.Thr597Ala)
HGVS:
  • NC_000023.11:g.74742768T>C
  • NG_027726.1:g.187685A>G
  • NM_001008537.3:c.1789A>GMANE SELECT
  • NP_001008537.1:p.Thr597Ala
  • NC_000023.10:g.73962603T>C
  • NM_001008537.2:c.1789A>G
Protein change:
T597A
Links:
dbSNP: rs752183295
NCBI 1000 Genomes Browser:
rs752183295
Molecular consequence:
  • NM_001008537.3:c.1789A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
X-linked intellectual disability, Cantagrel type (XLID98)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 98
Identifiers:
MONDO: MONDO:0010483; MedGen: C3806730; Orphanet: 85277; OMIM: 300912

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000773182Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 17, 2017) 		germlineclinical testing

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

Help

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

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000773182.1

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

Description

This sequence change replaces threonine with alanine at codon 597 of the KIAA2022 protein (p.Thr597Ala). The threonine residue is weakly conserved and there is a small physicochemical difference between threonine and alanine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with KIAA2022-related disease. 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 tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.

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

Last Updated: Aug 5, 2023