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NM_181486.4(TBX5):c.755G>C (p.Ser252Thr) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 8, 2015
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:
RCV000255260.1

Allele description [Variation Report for NM_181486.4(TBX5):c.755G>C (p.Ser252Thr)]

NM_181486.4(TBX5):c.755G>C (p.Ser252Thr)

Gene:
TBX5:T-box transcription factor 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q24.21
Genomic location:
Preferred name:
NM_181486.4(TBX5):c.755G>C (p.Ser252Thr)
HGVS:
  • NC_000012.12:g.114385476C>G
  • NG_007373.1:g.27967G>C
  • NM_000192.3:c.755G>C
  • NM_080717.4:c.605G>C
  • NM_181486.4:c.755G>CMANE SELECT
  • NP_000183.2:p.Ser252Thr
  • NP_542448.1:p.Ser202Thr
  • NP_852259.1:p.Ser252Thr
  • LRG_670t1:c.755G>C
  • LRG_670:g.27967G>C
  • LRG_670p1:p.Ser252Thr
  • NC_000012.11:g.114823281C>G
Protein change:
S202T
Links:
dbSNP: rs863223776
NCBI 1000 Genomes Browser:
rs863223776
Molecular consequence:
  • NM_000192.3:c.755G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080717.4:c.605G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181486.4:c.755G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000321955GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Dec 8, 2015) 		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, SCV000321955.6

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

Description

The S252T missense variant has not been previously reported as disease causing nor as a benign polymorphism. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. S252T alters the last base of exon 7, immediately 5' of the canonical GT" splice donor site. In silico analysis with several different splice algorithms predicts that this splice donor site is abolished or altered, potentially leading to aberrant gene splicing. In addition, two other nucleotide changes (G>T aka S252I and G>A aka S252N) at this highly conserved position have been seen in multiple patients referred for clinical testing for HOS at GeneDx. Although the effect of these variants on gene splicing has not yet been demonstrated, S252I has been reported in the literature in association with Holt-Oram syndrome (Cross et al., 2000). In summary, we consider S252T to be likely pathogenic; however, the possibility that it is benign cannot be excluded."

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

Last Updated: Jun 23, 2024