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NM_014112.5(TRPS1):c.2726G>A (p.Cys909Tyr) AND Trichorhinophalangeal syndrome type I or III

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 6, 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:
RCV002272981.2

Allele description [Variation Report for NM_014112.5(TRPS1):c.2726G>A (p.Cys909Tyr)]

NM_014112.5(TRPS1):c.2726G>A (p.Cys909Tyr)

Gene:
TRPS1:transcriptional repressor GATA binding 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q23.3
Genomic location:
Preferred name:
NM_014112.5(TRPS1):c.2726G>A (p.Cys909Tyr)
HGVS:
  • NC_000008.11:g.115418427C>T
  • NG_012383.3:g.255575G>A
  • NG_053427.1:g.61C>T
  • NM_001282902.3:c.2699G>A
  • NM_001282903.3:c.2705G>A
  • NM_001330599.2:c.2687G>A
  • NM_014112.5:c.2726G>AMANE SELECT
  • NP_001269831.1:p.Cys900Tyr
  • NP_001269832.1:p.Cys902Tyr
  • NP_001317528.1:p.Cys896Tyr
  • NP_054831.2:p.Cys909Tyr
  • NC_000008.10:g.116430655C>T
  • NM_014112.4:c.2726G>A
Protein change:
C896Y
Links:
dbSNP: rs2129769241
NCBI 1000 Genomes Browser:
rs2129769241
Molecular consequence:
  • NM_001282902.3:c.2699G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282903.3:c.2705G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330599.2:c.2687G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014112.5:c.2726G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Trichorhinophalangeal syndrome type I or III
Synonyms:
Trichorhinophalangeal syndrome type 1 and 3
Identifiers:
MedGen: C5231006

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002557494Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 6, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Trichorhinophalangeal syndrome type I: a novel mutation and Perthes-like changes of the hip in a family with 4 cases over 3 generations.

Hufeland M, Rahner N, Krauspe R.

J Pediatr Orthop. 2015 Jan;35(1):e1-5. doi: 10.1097/BPO.0000000000000330.

PubMed [citation]
PMID:
25333908

Proband-only medical exome sequencing as a cost-effective first-tier genetic diagnostic test for patients without prior molecular tests and clinical diagnosis in a developing country: the China experience.

Hu X, Li N, Xu Y, Li G, Yu T, Yao RE, Fu L, Wang J, Yin L, Yin Y, Wang Y, Jin X, Wang X, Wang J, Shen Y.

Genet Med. 2018 Sep;20(9):1045-1053. doi: 10.1038/gim.2017.195. Epub 2017 Nov 2.

PubMed [citation]
PMID:
29095814
See all PubMed Citations (3)

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557494.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with trichorhinophalangeal syndrome. (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from cysteine to tyrosine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants. Variant is located in the zinc binding site of the GATA zinc finger domain, which is correlated with type III trichorhinophalangeal syndrome (NCBI, PDB, PMID: 25333908). (SP) 0704 - Another missense variant comparable to the one identified in this case has limited previous evidence for pathogenicity. A different variant in the same codon resulting in a change to a serine has been reported in a de novo patient with trichorhinophalangeal syndrome (PMID: 29095814). (SP) 0803 - This variant has limited previous evidence of pathogenicity in two individuals from the same family with trichorhinophalangeal syndrome (PMID: 25333908). (SP) 1007 - No published functional evidence has been identified for this variant. (I) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Jan 26, 2024