NM_004273.5(CHST3):c.877G>T (p.Asp293Tyr) AND Spondyloepiphyseal dysplasia with congenital joint dislocations

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 18, 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:: RCV002815609.3

Allele description [Variation Report for NM_004273.5(CHST3):c.877G>T (p.Asp293Tyr)]

NM_004273.5(CHST3):c.877G>T (p.Asp293Tyr)

Gene:

CHST3:carbohydrate sulfotransferase 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_004273.5(CHST3):c.877G>T (p.Asp293Tyr)

HGVS:

NC_000010.11:g.72007908G>T
NG_012635.1:g.48547G>T
NM_004273.5:c.877G>TMANE SELECT
NP_004264.2:p.Asp293Tyr
NC_000010.10:g.73767666G>T

Protein change:

D293Y

Molecular consequence:

NM_004273.5:c.877G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Spondyloepiphyseal dysplasia with congenital joint dislocations (SEDCJD)
Synonyms:: Kozlowski Celermajer Tink syndrome; Humero-spinal dysostosis with congenital heart disease
Identifiers:: MONDO: MONDO:0007738; MedGen: C1837657; Orphanet: 263463; OMIM: 143095

Recent activity

Clear Turn Off Turn On

NPB neuropeptide B [Homo sapiens]
NPB neuropeptide B [Homo sapiens]
Gene ID:256933

Gene
Gene Links for GEO Profiles (Select 88155751) (1)
Gene
Macrolepiota aberdarense isolate KIA08 18S ribosomal RNA gene, partial sequence;...
Macrolepiota aberdarense isolate KIA08 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
gi|927544253|gb|KP974614.1|

Nucleotide
Homo sapiens preproprotein L7 (PPL7) precursor RNA, complete cds
Homo sapiens preproprotein L7 (PPL7) precursor RNA, complete cds
gi|32401242|gb|AF525738.1|

Nucleotide

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
SCV003207786	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 18, 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

SCV003207786

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 18, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003207786.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with CHST3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 293 of the CHST3 protein (p.Asp293Tyr).

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine