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NM_024665.7(TBL1XR1):c.441T>G (p.Asp147Glu) AND Intellectual disability, autosomal dominant 41

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 16, 2021
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:
RCV002227529.1

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.441T>G (p.Asp147Glu)]

NM_024665.7(TBL1XR1):c.441T>G (p.Asp147Glu)

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.441T>G (p.Asp147Glu)
HGVS:
  • NC_000003.12:g.177050597A>C
  • NG_047195.1:g.151664T>G
  • NM_001321193.3:c.441T>G
  • NM_001321194.3:c.441T>G
  • NM_001321195.3:c.180T>G
  • NM_001374327.1:c.441T>G
  • NM_001374328.1:c.441T>G
  • NM_001374329.1:c.441T>G
  • NM_001374330.1:c.180T>G
  • NM_024665.7:c.441T>GMANE SELECT
  • NP_001308122.1:p.Asp147Glu
  • NP_001308123.1:p.Asp147Glu
  • NP_001308124.1:p.Asp60Glu
  • NP_001361256.1:p.Asp147Glu
  • NP_001361257.1:p.Asp147Glu
  • NP_001361258.1:p.Asp147Glu
  • NP_001361259.1:p.Asp60Glu
  • NP_078941.2:p.Asp147Glu
  • NC_000003.11:g.176768385A>C
  • NM_001321194.1:c.441T>G
  • NM_024665.4:c.441T>G
Protein change:
D147E
Links:
dbSNP: rs1197826368
NCBI 1000 Genomes Browser:
rs1197826368
Molecular consequence:
  • NM_001321193.3:c.441T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321194.3:c.441T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321195.3:c.180T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374327.1:c.441T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374328.1:c.441T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374329.1:c.441T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374330.1:c.180T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024665.7:c.441T>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Intellectual disability, autosomal dominant 41 (MRD41)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 41
Identifiers:
MONDO: MONDO:0014842; MedGen: C4310784; Orphanet: 2823; OMIM: 616944

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002506922New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Apr 16, 2021) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002506922.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.441T>G (p.Asp147Glu) variant identified in the TBL1XR1 gene substitutes a moderately conserved Aspartic Acid for Glutamic Acid at amino acid 147/515 (exon 7/17). This variant is found with low frequency in gnomAD(v3.1.1) (1 heterozygote, 0 homozygotes; allele frequency: 6.57e-6) suggesting it is not a common benign variant in the populations represented in that database. In silico algorithms predict this variant to be Tolerated (SIFT; score:0.455) and Benign (REVEL; score: 0.105) to the function of the canonical transcript. This variant is absent from ClinVar and to our current knowledge has not been reported in affected individuals in the literature. The p.Asp147 residue is not within a mapped domain of TBL1XR1 (UniProtKB:Q9BZK7). Given the lack of compelling evidence for its pathogenicity, the c.441T>G (p.Asp147Glu) variant identified in the TBL1XR1 gene is reported as a Variant of Uncertain Significance.AS51

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024