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NM_001159773.2(CANT1):c.676G>A (p.Val226Met) AND Desbuquois dysplasia 1

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Jan 31, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000024010.8

Allele description [Variation Report for NM_001159773.2(CANT1):c.676G>A (p.Val226Met)]

NM_001159773.2(CANT1):c.676G>A (p.Val226Met)

Gene:
CANT1:calcium activated nucleotidase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.3
Genomic location:
Preferred name:
NM_001159773.2(CANT1):c.676G>A (p.Val226Met)
HGVS:
  • NC_000017.11:g.78995177C>T
  • NG_016645.1:g.19641G>A
  • NM_001159772.2:c.676G>A
  • NM_001159773.2:c.676G>AMANE SELECT
  • NM_138793.3:c.676G>A
  • NM_138793.4:c.676G>A
  • NP_001153244.1:p.Val226Met
  • NP_001153245.1:p.Val226Met
  • NP_620148.1:p.Val226Met
  • NC_000017.10:g.76991259C>T
  • NM_138793.4:c.676G>A
  • Q8WVQ1:p.Val226Met
Protein change:
V226M; VAL226MET
Links:
UniProtKB: Q8WVQ1#VAR_068659; OMIM: 613165.0013; dbSNP: rs377546036
NCBI 1000 Genomes Browser:
rs377546036
Molecular consequence:
  • NM_001159772.2:c.676G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001159773.2:c.676G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138793.4:c.676G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Desbuquois dysplasia 1 (DBQD1)
Synonyms:
MICROMELIC DWARFISM WITH VERTEBRAL AND METAPHYSEAL ABNORMALITIES AND ADVANCED CARPOTARSAL OSSIFICATION; DESBUQUOIS DYSPLASIA 1, KIM VARIANT
Identifiers:
MONDO: MONDO:0009629; MedGen: C4012146; Orphanet: 1425; OMIM: 251450

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000045301OMIM
no assertion criteria provided
Pathogenic
(May 1, 2011)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV002518636Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2019)
Pathogenic
(May 4, 2022)
germlineclinical testing

Citation Link,

SCV004804085Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Jan 31, 2024)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A variant of Desbuquois dysplasia characterized by advanced carpal bone age, short metacarpals, and elongated phalanges: report of seven cases.

Kim OH, Nishimura G, Song HR, Matsui Y, Sakazume S, Yamada M, Narumi Y, Alanay Y, Unger S, Cho TJ, Park SS, Ikegawa S, Meinecke P, Superti-Furga A.

Am J Med Genet A. 2010 Apr;152A(4):875-85. doi: 10.1002/ajmg.a.33347.

PubMed [citation]
PMID:
20358597

A founder mutation of CANT1 common in Korean and Japanese Desbuquois dysplasia.

Dai J, Kim OH, Cho TJ, Miyake N, Song HR, Karasugi T, Sakazume S, Ikema M, Matsui Y, Nagai T, Matsumoto N, Ohashi H, Kamatani N, Nishimura G, Furuichi T, Takahashi A, Ikegawa S.

J Hum Genet. 2011 May;56(5):398-400. doi: 10.1038/jhg.2011.28. Epub 2011 Mar 17.

PubMed [citation]
PMID:
21412251
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000045301.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

Desbuquois Dysplasia 1, Kim Variant

In a Japanese patient, born of consanguineous parents, with the Kim variant of Desbuquois dysplasia-1 (DBQD1; see 251450), Furuichi et al. (2011) identified a homozygous 676G-A transition in the CANT1 gene, resulting in a val226-to-met (V226M) substitution in a highly conserved residue. Four additional patients, of Japanese or Korean origin, with this phenotype also carried the V226M substitution in compound heterozygosity with another pathogenic mutation in the CANT1 gene (see, e.g., 613165.0014). The V226M mutation was found in 1 of 754 Japanese controls and in 1 of 187 Korean controls. Four of the 5 patients had been reported by Kim et al. (2010) as having a milder form of the disorder. All had normal cognitive development, but most showed delayed motor development. All had short stature and multiple joint dislocations and laxity, particularly affecting the knee. Radiographic criteria included a 'monkey wrench' appearance of the proximal femora, epimetaphyseal dysplasia at the knees, and advanced carpal/tarsal bone age. Radiographic studies showed short metacarpals with normal or slightly elongated proximal and middle phalanges and short distal phalanges, resulting in a nearly equal length of the second to fourth or fifth finger. None had an accessory ossification center or thumb anomalies. After about age 15 years, radiographs showed precocious degenerative arthritis in the carpal bones and interphalangeal joints. The hip joints showed premature degenerative osteoarthritis with age. All patients also had kyphoscoliosis with vertebral endplate irregularities and narrowing of the disc space; the older ones developed progressive degenerative spondylosis. In vitro functional expression studies in COS-7 cells showed that the V226M mutant protein was stably expressed and secreted normally, but had decreased enzyme activity compared to wildtype. The findings indicated that the so-called Kim variant of DBQD is allelic to types 1 and 2 DBQD.

By haplotype analysis of the 5 families with the V226M mutation reported by Furuichi et al. (2011), Dai et al. (2011) demonstrated a founder effect for this mutation among Japanese and Korean individuals. The age of the mutation was estimated at about 1,420 years, around the time of the late Kofun era.

Epiphyseal Dysplasia, Multiple, 7

In a female patient of Latino origin (R01-152A) with multiple epiphyseal dysplasia (EDM7; 617719), Balasubramanian et al. (2017) identified homozygosity for the V226M mutation in the CANT1 gene. The authors stated that although radiographs of the EDM patient showed some overlapping features with DBQD, the overall phenotype was milder and clearly distinct from DBQD. They noted that 1 previously reported family with the Kim variant of DBQD was also homozygous for V226M (Furuichi et al., 2011), but stated that radiographic data for a full comparison of the phenotype with their EDM case had not been published.

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

From Mendelics, SCV002518636.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004804085.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: CANT1 c.676G>A (p.Val226Met) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.8e-05 in 251052 control chromosomes (gnomAD). c.676G>A has been reported in the literature in multiple individuals affected with Desbuquois dysplasia or Multiple Epiphyseal Dysplasia (Furuichi_2011, Balasubramanian_2017). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, finding that the variant results in a substantial reduction of normal nucleotidase activity (Furuichi_2011). The following publications have been ascertained in the context of this evaluation (PMID: 21037275, 28742282). ClinVar contains an entry for this variant (Variation ID: 31018). Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Apr 6, 2024