NM_014112.5(TRPS1):c.2031A>C (p.Lys677Asn) AND Trichorhinophalangeal dysplasia type I

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 19, 2022
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:: RCV002640758.1

Allele description [Variation Report for NM_014112.5(TRPS1):c.2031A>C (p.Lys677Asn)]

NM_014112.5(TRPS1):c.2031A>C (p.Lys677Asn)

Genes:

TRPS1-AS1:TRPS1 antisense RNA 1 [Gene - HGNC]
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.2031A>C (p.Lys677Asn)

Other names:

p.Lys677Asn

HGVS:

NC_000008.11:g.115603938T>G
NG_012383.3:g.70064A>C
NM_001282902.3:c.2004A>C
NM_001282903.3:c.2010A>C
NM_001330599.2:c.1992A>C
NM_014112.5:c.2031A>CMANE SELECT
NP_001269831.1:p.Lys668Asn
NP_001269832.1:p.Lys670Asn
NP_001317528.1:p.Lys664Asn
NP_054831.2:p.Lys677Asn
NC_000008.10:g.116616165T>G

Protein change:

K664N

Molecular consequence:

NM_001282902.3:c.2004A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282903.3:c.2010A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001330599.2:c.1992A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_014112.5:c.2031A>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003194729	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 19, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003194729

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 19, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV003194729.1

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

Description

A heterozygous missense variation in exon 4 of the TRPS1 gene that results in the amino acid substitution of Asparagine for Lysine at codon 677 (p.Lys677Asn) was detected. The p.Lys677Asn variant has not been reported in the 1000 genomes, gnomAD databases. The in silico predictions of the variant are possibly damaging by PolyPhen-2 (HumDiv) and damaging by SIFT. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as a variant of uncertain significance.

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

Last Updated: Oct 14, 2023

ClinVar

Relating variation to medicine