NM_000493.4(COL10A1):c.1832G>A (p.Trp611Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 3, 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:: RCV003556046.2

Allele description [Variation Report for NM_000493.4(COL10A1):c.1832G>A (p.Trp611Ter)]

NM_000493.4(COL10A1):c.1832G>A (p.Trp611Ter)

Genes:

NT5DC1:5'-nucleotidase domain containing 1 [Gene - HGNC]
COL10A1:collagen type X alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q22.1

Genomic location:

Preferred name:

NM_000493.4(COL10A1):c.1832G>A (p.Trp611Ter)

HGVS:

NC_000006.12:g.116120284C>T
NG_008032.1:g.10850G>A
NG_021351.1:g.24449C>T
NG_021351.2:g.24433C>T
NM_000493.4:c.1832G>AMANE SELECT
NM_001424106.1:c.1832G>A
NM_001424107.1:c.1832G>A
NM_152729.3:c.529+2339C>TMANE SELECT
NP_000484.2:p.Trp611Ter
NP_001411035.1:p.Trp611Ter
NP_001411036.1:p.Trp611Ter
NC_000006.11:g.116441447C>T

Protein change:

W611*; TRP611TER

Links:

OMIM: 120110.0019; dbSNP: rs111033556

NCBI 1000 Genomes Browser:

rs111033556

Molecular consequence:

NM_152729.3:c.529+2339C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000493.4:c.1832G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001424106.1:c.1832G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001424107.1:c.1832G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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
SCV004294675	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 3, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12554676, 36400164, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004294675

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 3, 2023)

germline

clinical testing

PubMed (3)
[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

Tissue-specific RNA surveillance? Nonsense-mediated mRNA decay causes collagen X haploinsufficiency in Schmid metaphyseal chondrodysplasia cartilage.

Bateman JF, Freddi S, Nattrass G, Savarirayan R.

Hum Mol Genet. 2003 Feb 1;12(3):217-25.

PubMed [citation]

PMID:: 12554676

Natural history and genetic spectrum of the Turkish metaphyseal dysplasia cohort, including rare types caused by biallelic COL10A1, COL2A1, and LBR variants.

Tüysüz B, Kasap B, Sarıtaş M, Alkaya DU, Bozlak S, Kıykım A, Durmaz A, Yıldırım T, Akpınar E, Apak H, Vural M.

Bone. 2023 Feb;167:116614. doi: 10.1016/j.bone.2022.116614. Epub 2022 Nov 15.

PubMed [citation]

PMID:: 36400164

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004294675.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Trp611*) in the COL10A1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 70 amino acid(s) of the COL10A1 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with autosomal dominant Schmid-type metaphyseal chondrodysplasia and/or Schmid metaphyseal chondrodysplasia (PMID: 12554676, 36400164). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 17482). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. For these reasons, this variant has been classified as Pathogenic.

#	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