NM_001111125.3(IQSEC2):c.2477T>C (p.Met826Thr) AND Intellectual disability, X-linked 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 10, 2014
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:: RCV000449548.1

Allele description [Variation Report for NM_001111125.3(IQSEC2):c.2477T>C (p.Met826Thr)]

NM_001111125.3(IQSEC2):c.2477T>C (p.Met826Thr)

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.2477T>C (p.Met826Thr)

HGVS:

NC_000023.11:g.53248219A>G
NG_021296.2:g.78132T>C
NM_001111125.3:c.2477T>CMANE SELECT
NM_015075.2:c.1862T>C
NP_001104595.1:p.Met826Thr
NP_055890.1:p.Met621Thr
LRG_1194t1:c.2477T>C
LRG_1194:g.78132T>C
LRG_1194p1:p.Met826Thr
NC_000023.10:g.53277401A>G
NM_001111125.2:c.2477T>C

Protein change:

M621T

Links:

dbSNP: rs1060499660

NCBI 1000 Genomes Browser:

rs1060499660

Molecular consequence:

NM_001111125.3:c.2477T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_015075.2:c.1862T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000537719	Center of Genomic medicine, Geneva, University Hospital of Geneva	criteria provided, single submitter (MacArthur et al. (Nature 2014))	Pathogenic (Nov 10, 2014)	maternal	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

SCV000537719

Center of Genomic medicine, Geneva, University Hospital of Geneva

criteria provided, single submitter

(MacArthur et al. (Nature 2014))

Pathogenic
(Nov 10, 2014)

maternal

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	maternal	yes	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Guidelines for investigating causality of sequence variants in human disease.

MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, et al.

Nature. 2014 Apr 24;508(7497):469-76. doi: 10.1038/nature13127.

PubMed [citation]

PMID:: 24759409
PMCID:: PMC4180223

Details of each submission

From Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV000537719.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

Last Updated: May 19, 2024

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