NM_024665.7(TBL1XR1):c.1496G>A (p.Gly499Glu) AND Intellectual disability

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 10, 2020
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:: RCV001260791.2

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.1496G>A (p.Gly499Glu)]

NM_024665.7(TBL1XR1):c.1496G>A (p.Gly499Glu)

Gene:

TBL1XR1:TBL1X/Y related 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q26.32

Genomic location:

Preferred name:

NM_024665.7(TBL1XR1):c.1496G>A (p.Gly499Glu)

HGVS:

NC_000003.12:g.177026395C>T
NG_047195.1:g.175866G>A
NM_001321193.3:c.1496G>A
NM_001321194.3:c.1496G>A
NM_001321195.3:c.1235G>A
NM_001374327.1:c.1496G>A
NM_001374328.1:c.1496G>A
NM_001374329.1:c.1496G>A
NM_001374330.1:c.1235G>A
NM_024665.7:c.1496G>AMANE SELECT
NP_001308122.1:p.Gly499Glu
NP_001308123.1:p.Gly499Glu
NP_001308124.1:p.Gly412Glu
NP_001361256.1:p.Gly499Glu
NP_001361257.1:p.Gly499Glu
NP_001361258.1:p.Gly499Glu
NP_001361259.1:p.Gly412Glu
NP_078941.2:p.Gly499Glu
NC_000003.11:g.176744183C>T
NM_024665.5:c.1496G>A

Protein change:

G412E

Links:

dbSNP: rs1713131684

NCBI 1000 Genomes Browser:

rs1713131684

Molecular consequence:

NM_001321193.3:c.1496G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001321194.3:c.1496G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001321195.3:c.1235G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374327.1:c.1496G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374328.1:c.1496G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374329.1:c.1496G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374330.1:c.1235G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024665.7:c.1496G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Intellectual disability
Synonyms:: Intellectual functioning disability; intellectual disabilities; Intellectual developmental disorder
Identifiers:: MONDO: MONDO:0001071; MeSH: D008607; MedGen: C3714756; Human Phenotype Ontology: HP:0001249

Recent activity

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sterol O-acyltransferase 1 isoform X1 [Mus musculus]
sterol O-acyltransferase 1 isoform X1 [Mus musculus]
gi|568910598|ref|XP_006496782.1|

Protein
transmembrane protein 18 isoform 2 [Homo sapiens]
transmembrane protein 18 isoform 2 [Homo sapiens]
gi|1208914960|ref|NP_001339609.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001437884	Diagnostic Laboratory, Strasbourg University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 10, 2020)	de novo	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

SCV001437884

Diagnostic Laboratory, Strasbourg University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 10, 2020)

de novo

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	de novo	yes	1	not provided	not provided	1	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 Diagnostic Laboratory, Strasbourg University Hospital, SCV001437884.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	de novo	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 30, 2023

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