NM_014112.5(TRPS1):c.801del (p.Arg268fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 13, 2023
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:: RCV003800284.1

Allele description [Variation Report for NM_014112.5(TRPS1):c.801del (p.Arg268fs)]

NM_014112.5(TRPS1):c.801del (p.Arg268fs)

Gene:

TRPS1:transcriptional repressor GATA binding 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8q23.3

Genomic location:

Preferred name:

NM_014112.5(TRPS1):c.801del (p.Arg268fs)

HGVS:

NC_000008.11:g.115619298del
NG_012383.3:g.54705del
NM_001282902.3:c.774del
NM_001282903.3:c.780del
NM_001330599.2:c.762del
NM_014112.5:c.801delMANE SELECT
NP_001269831.1:p.Arg259fs
NP_001269832.1:p.Arg261fs
NP_001317528.1:p.Arg255fs
NP_054831.2:p.Arg268fs
NC_000008.10:g.116631524del
NC_000008.10:g.116631525del

Protein change:

R255fs

Molecular consequence:

NM_001282902.3:c.774del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282903.3:c.780del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330599.2:c.762del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014112.5:c.801del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Trichorhinophalangeal syndrome, type III (TRPS3)
Synonyms:: Trichorhinophalangeal syndrome type 3; TRPS 3; Sugio-Kajii Syndrome
Identifiers:: MONDO: MONDO:0008597; MedGen: C1860823; Orphanet: 77258; OMIM: 190351

Name:: Trichorhinophalangeal dysplasia type I (TRPS1)
Synonyms:: TRPS I; Trichorhinophalangeal syndrome type 1; Giedion syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008596; MedGen: C0432233; Orphanet: 77258; OMIM: 190350

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004593220	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 13, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11112658, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004593220

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 13, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genotypic and phenotypic spectrum in tricho-rhino-phalangeal syndrome types I and III.

Lüdecke HJ, Schaper J, Meinecke P, Momeni P, Gross S, von Holtum D, Hirche H, Abramowicz MJ, Albrecht B, Apacik C, Christen HJ, Claussen U, Devriendt K, Fastnacht E, Forderer A, Friedrich U, Goodship TH, Greiwe M, Hamm H, Hennekam RC, Hinkel GK, Hoeltzenbein M, et al.

Am J Hum Genet. 2001 Jan;68(1):81-91. Epub 2000 Dec 7.

PubMed [citation]

PMID:: 11112658
PMCID:: PMC1234936

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004593220.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with TRPS1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg268Glyfs*48) in the TRPS1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TRPS1 are known to be pathogenic (PMID: 11112658).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 5, 2024

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