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NM_000523.4(HOXD13):c.782-2del AND Synpolydactyly type 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 15, 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:
RCV000015999.21

Allele description [Variation Report for NM_000523.4(HOXD13):c.782-2del]

NM_000523.4(HOXD13):c.782-2del

Gene:
HOXD13:homeobox D13 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2q31.1
Genomic location:
Preferred name:
NM_000523.4(HOXD13):c.782-2del
HGVS:
  • NC_000002.12:g.176094478del
  • NG_008137.1:g.6675del
  • NM_000523.4:c.782-2delMANE SELECT
  • NC_000002.11:g.176959206del
  • NM_000523.3:c.782-2del
Links:
OMIM: 142989.0006; dbSNP: rs764838478
NCBI 1000 Genomes Browser:
rs764838478
Molecular consequence:
  • NM_000523.4:c.782-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Synpolydactyly type 1
Identifiers:
MONDO: MONDO:0008513; MedGen: C5574994; OMIM: 186000

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000036266OMIM
no assertion criteria provided
Pathogenic
(Aug 15, 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

An acceptor splice site mutation in HOXD13 results in variable hand, but consistent foot malformations.

Kan SH, Johnson D, Giele H, Wilkie AO.

Am J Med Genet A. 2003 Aug 15;121A(1):69-74.

PubMed [citation]
PMID:
12900906

Deletions in HOXD13 segregate with an identical, novel foot malformation in two unrelated families.

Goodman F, Giovannucci-Uzielli ML, Hall C, Reardon W, Winter R, Scambler P.

Am J Hum Genet. 1998 Oct;63(4):992-1000.

PubMed [citation]
PMID:
9758628
PMCID:
PMC1377502

Details of each submission

From OMIM, SCV000036266.2

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

Description

Kan et al. (2003) screened for mutations of the HOXD13 gene in patients with a variety of limb malformations. In a 3-generation family without the typical synpolydactyly phenotype in the hands, but with bilateral partial duplication of the second metatarsals within the first web space of the feet (SPD1; 186000), they identified a heterozygous deletion of an adenine at position -2 in the acceptor splice site of exon 2, which they referred to as 758-2delA. Kan et al. (2003) noted that the foot abnormality in this family was similar to that described in 2 families by Goodman et al. (1998) in which different deletions of HOXD13 were found (142989.0002; 142989.0003), and suggested that the distinctive foot phenotype occurs as a result of haploinsufficiency of HOXD13.

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

Last Updated: Jul 29, 2023