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NM_024665.7(TBL1XR1):c.1256C>T (p.Ser419Phe) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 28, 2017
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:
RCV000519529.1

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.1256C>T (p.Ser419Phe)]

NM_024665.7(TBL1XR1):c.1256C>T (p.Ser419Phe)

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.1256C>T (p.Ser419Phe)
HGVS:
  • NC_000003.12:g.177033131G>A
  • NG_047195.1:g.169130C>T
  • NM_001321193.3:c.1256C>T
  • NM_001321194.3:c.1256C>T
  • NM_001321195.3:c.995C>T
  • NM_001374327.1:c.1256C>T
  • NM_001374328.1:c.1256C>T
  • NM_001374329.1:c.1256C>T
  • NM_001374330.1:c.995C>T
  • NM_024665.7:c.1256C>TMANE SELECT
  • NP_001308122.1:p.Ser419Phe
  • NP_001308123.1:p.Ser419Phe
  • NP_001308124.1:p.Ser332Phe
  • NP_001361256.1:p.Ser419Phe
  • NP_001361257.1:p.Ser419Phe
  • NP_001361258.1:p.Ser419Phe
  • NP_001361259.1:p.Ser332Phe
  • NP_078941.2:p.Ser419Phe
  • NC_000003.11:g.176750919G>A
  • NM_024665.4:c.1256C>T
Protein change:
S332F
Links:
dbSNP: rs1553808356
NCBI 1000 Genomes Browser:
rs1553808356
Molecular consequence:
  • NM_001321193.3:c.1256C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321194.3:c.1256C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321195.3:c.995C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374327.1:c.1256C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374328.1:c.1256C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374329.1:c.1256C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374330.1:c.995C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024665.7:c.1256C>T - 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
SCV000619448GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jul 28, 2017) 		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, SCV000619448.2

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

Description

The S419F variant in the TBL1XR1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The S419F 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. In addition, this substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret S419F as a variant of uncertain significance.

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

Last Updated: Apr 23, 2022