NM_000523.4(HOXD13):c.781+1G>A AND Synpolydactyly type 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 12, 2016
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:: RCV000210954.3

Allele description [Variation Report for NM_000523.4(HOXD13):c.781+1G>A]

NM_000523.4(HOXD13):c.781+1G>A

Gene:

HOXD13:homeobox D13 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.1

Genomic location:

Preferred name:

NM_000523.4(HOXD13):c.781+1G>A

HGVS:

NC_000002.12:g.176093672G>A
NG_008137.1:g.5869G>A
NM_000523.4:c.781+1G>AMANE SELECT
NC_000002.11:g.176958400G>A

Nucleotide change:

IVS1, G-A, +1

Links:

OMIM: 142989.0016; dbSNP: rs886037831

NCBI 1000 Genomes Browser:

rs886037831

Molecular consequence:

NM_000523.4:c.781+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

Recent activity

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Oncorhynchus mykiss haplotype NEW09 D-loop, partial sequence; tRNA-Phe (trnF) ge...
Oncorhynchus mykiss haplotype NEW09 D-loop, partial sequence; tRNA-Phe (trnF) gene, complete sequence; and 12S ribosomal RNA gene, partial sequence; mitochondrial
gi|299735179|gb|HM229330.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267636	OMIM	no assertion criteria provided	Pathogenic (Aug 12, 2016)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267636

OMIM

no assertion criteria provided

Pathogenic
(Aug 12, 2016)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

A splice donor site mutation in HOXD13 underlies synpolydactyly with cortical bone thinning.

Shi X, Ji C, Cao L, Wu Y, Shang Y, Wang W, Luo Y.

Gene. 2013 Dec 15;532(2):297-301. doi: 10.1016/j.gene.2013.09.040. Epub 2013 Sep 18.

PubMed [citation]

PMID:: 24055421

Details of each submission

From OMIM, SCV000267636.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 5 affected members of a 4-generation Chinese family with mild synpolydactyly as well as broad halluces with cortical bone thinning of the proximal phalanges (SPD1; 186000), Shi et al. (2013) identified heterozygosity for a splice site mutation (c.781+1G-A) that activates a cryptic splice site, resulting in skipping of the last 214 nucleotides of exon 1, causing a frameshift and creating a premature stop codon (Gly190fsTer4). The mutation was not found in 3 unaffected family members or in 60 ethnically matched controls. The mutant showed a significantly lower level of transcriptional activity than wildtype in dual-luciferase assay.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 29, 2023

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