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NM_024665.7(TBL1XR1):c.1109A>G (p.Asp370Gly) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 1, 2016
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:
RCV000497717.1

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.1109A>G (p.Asp370Gly)]

NM_024665.7(TBL1XR1):c.1109A>G (p.Asp370Gly)

Genes:
LOC126806878:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:176755168-176756367 [Gene]
TBL1XR1:TBL1X/Y related 1 [Gene - OMIM - HGNC]
TBL1XR1-AS1:TBL1XR1 antisense RNA 1 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q26.32
Genomic location:
Preferred name:
NM_024665.7(TBL1XR1):c.1109A>G (p.Asp370Gly)
HGVS:
  • NC_000003.12:g.177038111T>C
  • NG_047195.1:g.164150A>G
  • NM_001321193.3:c.1109A>G
  • NM_001321194.3:c.1109A>G
  • NM_001321195.3:c.848A>G
  • NM_001374327.1:c.1109A>G
  • NM_001374328.1:c.1109A>G
  • NM_001374329.1:c.1109A>G
  • NM_001374330.1:c.848A>G
  • NM_024665.7:c.1109A>GMANE SELECT
  • NP_001308122.1:p.Asp370Gly
  • NP_001308123.1:p.Asp370Gly
  • NP_001308124.1:p.Asp283Gly
  • NP_001361256.1:p.Asp370Gly
  • NP_001361257.1:p.Asp370Gly
  • NP_001361258.1:p.Asp370Gly
  • NP_001361259.1:p.Asp283Gly
  • NP_078941.2:p.Asp370Gly
  • NC_000003.11:g.176755899T>C
  • NM_024665.4:c.1109A>G
Protein change:
D283G
Links:
dbSNP: rs1553810149
NCBI 1000 Genomes Browser:
rs1553810149
Molecular consequence:
  • NM_001321193.3:c.1109A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321194.3:c.1109A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321195.3:c.848A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374327.1:c.1109A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374328.1:c.1109A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374329.1:c.1109A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374330.1:c.848A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024665.7:c.1109A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000589875GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Jun 1, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000589875.2

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

Description

The D370G variant in the TBL1XR1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The D370G variant was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The D370G variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret D370G as strong candidate for a pathogenic variant

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

Last Updated: Mar 26, 2023