NM_001111125.3(IQSEC2):c.4387G>A (p.Ala1463Thr) AND Intellectual disability, X-linked 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 25, 2024
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:: RCV003989052.3

Allele description [Variation Report for NM_001111125.3(IQSEC2):c.4387G>A (p.Ala1463Thr)]

NM_001111125.3(IQSEC2):c.4387G>A (p.Ala1463Thr)

Gene:

IQSEC2:IQ motif and Sec7 domain ArfGEF 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.22

Genomic location:

Preferred name:

NM_001111125.3(IQSEC2):c.4387G>A (p.Ala1463Thr)

HGVS:

NC_000023.11:g.53234299C>T
NG_021296.2:g.92052G>A
NM_001111125.3:c.4387G>AMANE SELECT
NM_001410736.1:c.*872G>A
NM_015075.2:c.*872G>A
NP_001104595.1:p.Ala1463Thr
LRG_1194t1:c.4387G>A
LRG_1194:g.92052G>A
LRG_1194p1:p.Ala1463Thr
NC_000023.10:g.53263481C>T
NM_001111125.1:c.4387G>A

Protein change:

A1463T

Molecular consequence:

NM_001410736.1:c.*872G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_015075.2:c.*872G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001111125.3:c.4387G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Intellectual disability, X-linked 1 (XLID1)
Synonyms:: Mental retardation, X-linked, nonspecific; Atkin Flaitz Patil Smith syndrome; MENTAL RETARDATION, X-LINKED 18; See all synonyms [MedGen]
Identifiers:: Gene: 170530; MONDO: MONDO:0010656; MedGen: C2931498; Orphanet: 777; OMIM: 309530

Recent activity

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UNVERIFIED: Aepyceros melampus isolate 818-R cytochrome b-like (cytb) gene, part...
UNVERIFIED: Aepyceros melampus isolate 818-R cytochrome b-like (cytb) gene, partial sequence; mitochondrial
gi|1894664015|gb|MN969897.1|

Nucleotide
Social Environment
Social Environment
The aggregate of social and cultural institutions, forms, patterns, and processes that influence the life of an individual or community.<br/>Year introduced: 1973(1972)

MeSH
Genes, rRNA
Genes, rRNA
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPE...<br/>Year introduced: 1999

MeSH
Genes, vpu
Genes, vpu
DNA sequences that form the coding region for the HIV-1 regulatory protein vpu (viral protein U) that greatly increases the export of virus particles from infected cells. The ...<br/>Year introduced: 1991

MeSH
Genes, T-Cell Receptor gamma
Genes, T-Cell Receptor gamma
DNA sequences encoding the gamma chain of the T-cell receptor. The human gamma-chain locus is organized similarly to the TcR beta-chain locus.<br/>Year introduced: 1998

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004805551	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 25, 2024)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004805551

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 25, 2024)

germline

research

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	research

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 Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004805551.2

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

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

Last Updated: Aug 4, 2024

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