NM_001008537.3(NEXMIF):c.4271C>T (p.Ser1424Phe) AND X-linked intellectual disability, Cantagrel type

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 17, 2019
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:: RCV001332647.1

Allele description [Variation Report for NM_001008537.3(NEXMIF):c.4271C>T (p.Ser1424Phe)]

NM_001008537.3(NEXMIF):c.4271C>T (p.Ser1424Phe)

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.4271C>T (p.Ser1424Phe)

HGVS:

NC_000023.11:g.74740286G>A
NG_027726.1:g.190167C>T
NM_001008537.3:c.4271C>TMANE SELECT
NP_001008537.1:p.Ser1424Phe
NC_000023.10:g.73960121G>A
NM_001008537.2:c.4271C>T

Protein change:

S1424F

Links:

dbSNP: rs2080097689

NCBI 1000 Genomes Browser:

rs2080097689

Molecular consequence:

NM_001008537.3:c.4271C>T - 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

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polypeptide N-acetylgalactosaminyltransferase-like 6 isoform X3 [Homo sapiens]
polypeptide N-acetylgalactosaminyltransferase-like 6 isoform X3 [Homo sapiens]
gi|2462597345|ref|XP_054206066.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001525026	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 17, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001525026

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 17, 2019)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Baylor Genetics, SCV001525026.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 5, 2023

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