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NM_001008537.3(NEXMIF):c.1417T>C (p.Ser473Pro) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 12, 2022
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:
RCV002509545.1

Allele description [Variation Report for NM_001008537.3(NEXMIF):c.1417T>C (p.Ser473Pro)]

NM_001008537.3(NEXMIF):c.1417T>C (p.Ser473Pro)

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.1417T>C (p.Ser473Pro)
HGVS:
  • NC_000023.11:g.74743140A>G
  • NG_027726.1:g.187313T>C
  • NM_001008537.3:c.1417T>CMANE SELECT
  • NP_001008537.1:p.Ser473Pro
  • NC_000023.10:g.73962975A>G
  • NM_001008537.1:c.1417T>C
  • NM_001008537.2:c.1417T>C
Protein change:
S473P
Links:
dbSNP: rs891017786
NCBI 1000 Genomes Browser:
rs891017786
Molecular consequence:
  • NM_001008537.3:c.1417T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002819472Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Dec 12, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002819472.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: NEXMIF c.1417T>C (p.Ser473Pro) results in a non-conservative amino acid change located in the DUF4683 domain (domain of unknown function, IPR032757) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 182164 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1417T>C in individuals affected with Intellectual Developmental Disorder, X-Linked 98 and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Sep 29, 2024