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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

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Assertion and evidence details

Help
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]

Help

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