U.S. flag

An official website of the United States government

NM_000493.4(COL10A1):c.1896C>A (p.Tyr632Ter) AND Metaphyseal chondrodysplasia, Schmid type

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 1, 2003
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000019030.26

Allele description [Variation Report for NM_000493.4(COL10A1):c.1896C>A (p.Tyr632Ter)]

NM_000493.4(COL10A1):c.1896C>A (p.Tyr632Ter)

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.1896C>A (p.Tyr632Ter)
HGVS:
  • NC_000006.12:g.116120220G>T
  • NG_008032.1:g.10914C>A
  • NG_021351.1:g.24385G>T
  • NG_021351.2:g.24369G>T
  • NM_000493.4:c.1896C>AMANE SELECT
  • NM_001424106.1:c.1896C>A
  • NM_001424107.1:c.1896C>A
  • NM_152729.3:c.529+2275G>TMANE SELECT
  • NP_000484.2:p.Tyr632Ter
  • NP_001411035.1:p.Tyr632Ter
  • NP_001411036.1:p.Tyr632Ter
  • NC_000006.11:g.116441383G>T
Protein change:
Y632*; TYR632TER
Links:
OMIM: 120110.0015; dbSNP: rs111033548
NCBI 1000 Genomes Browser:
rs111033548
Molecular consequence:
  • NM_152729.3:c.529+2275G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000493.4:c.1896C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001424106.1:c.1896C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001424107.1:c.1896C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Metaphyseal chondrodysplasia, Schmid type (MCDS)
Synonyms:
SPONDYLOMETAPHYSEAL DYSPLASIA, JAPANESE TYPE
Identifiers:
MONDO: MONDO:0007983; MedGen: C0265289; Orphanet: 174; OMIM: 156500

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000039317OMIM
no assertion criteria provided
Pathogenic
(Feb 1, 2003)
germlineliterature only

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

A nonsense mutation in the carboxyl-terminal domain of type X collagen causes haploinsufficiency in schmid metaphyseal chondrodysplasia.

Chan D, Weng YM, Graham HK, Sillence DO, Bateman JF.

J Clin Invest. 1998 Apr 1;101(7):1490-9.

PubMed [citation]
PMID:
9525992
PMCID:
PMC508727

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

Details of each submission

From OMIM, SCV000039317.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Chan et al. (1998) obtained growth plate cartilage from a patient with Schmid metaphyseal chondrodysplasia (MCDS; 156500), determined the type of collagen X mutation, and analyzed the expression of mutant and normal type X collagen mRNA and protein. The mutation was found to be a single nucleotide substitution that changed the tyr632 codon (TAC) to a stop codon (TAA). However, analysis of the expression of the normal and mutant allele transcripts in growth plate cartilage by reverse transcription PCR, restriction enzyme mapping, and a single nucleotide primer extension assay demonstrated that only normal mRNA was present. The lack of mutant mRNA is most likely the result of nonsense-mediated mRNA decay, a common fate of transcripts carrying premature termination mutations. Furthermore, no mutant protein was detected by immunoblotting cartilage extracts. The data indicated that a functionally null allele leading to type X collagen haploinsufficiency is the molecular basis of MCDS in this patient.

Bateman et al. (2003) demonstrated that Y632X mutant mRNA underwent nonsense-mediated decay in cartilage tissue but not in noncartilage cells.

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

Last Updated: Sep 29, 2024