chr2-176093094-G-GGCGGCGGCTGCGGCGGCGGCA

Variant names:

• chr2-176093094-G-GGCGGCGGCTGCGGCGGCGGCA
• rs878854345
• NM_000523.4:c.209_210insGGCTGCGGCGGCGGCAGCGGC

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 8P and 1B. PP5_Very_Strong BP3

The NM_000523.4(HOXD13):​c.209_210insGGCTGCGGCGGCGGCAGCGGC​(p.Ala64_Ala70dup) variant causes a disruptive inframe insertion change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: HOXD13 NM_000523.4 disruptive_inframe_insertion
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 3.98
• Publications: 1 publications found

Genes affected

HOXD13 (HGNC:5136): (homeobox D13) This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. Mutations in this particular gene cause synpolydactyly. [provided by RefSeq, Jul 2008]

HOXD13 Gene-Disease associations (from GenCC):

• brachydactyly-syndactyly syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Laboratory for Molecular Medicine
• synpolydactyly type 1

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• brachydactyly type E

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• syndactyly type 5

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_pathogenic. The variant received 7 ACMG points.

• PP5: Variant 2-176093094-G-GGCGGCGGCTGCGGCGGCGGCA is Pathogenic according to our data. Variant chr2-176093094-G-GGCGGCGGCTGCGGCGGCGGCA is described in ClinVar as Pathogenic. ClinVar VariationId is 14873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP3: Nonframeshift variant in repetitive region in NM_000523.4

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HOXD13	NM_000523.4	c.209_210insGGCTGCGGCGGCGGCAGCGGC	p.Ala64_Ala70dup	disruptive_inframe_insertion	Exon 1 of 2	ENST00000392539.4	NP_000514.2
HOXD13	XM_011511068.3	c.725-1381_725-1380insGGCTGCGGCGGCGGCAGCGGC		intron_variant	Intron 1 of 1		XP_011509370.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HOXD13	ENST00000392539.4	c.209_210insGGCTGCGGCGGCGGCAGCGGC	p.Ala64_Ala70dup	disruptive_inframe_insertion	Exon 1 of 2	1	NM_000523.4	ENSP00000376322.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Syndactyly type 5 Pathogenic:2

Apr 13, 2023

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 01, 2005

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Synpolydactyly type 1 Pathogenic:1

Mar 25, 2021

Institute for Genomic Medicine, Nationwide Children's Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

The c.209_210insGGCTGCGGCGGCGGCAGCGGC variant is predicted to cause a 7-residue expansion of the polyalanine tract in exon 1 of HOXD13. This variant was first reported to cause dominant synpolydactyly more than 20 years ago and has been described in multiple unrelated synpolydactyly kindreds (PMID: 9207113). In our research study, we sequenced three members of a family with four documented generations of polysyndactyly. After identifying a similar variant (9-alanine dup) in a different family with this condition, we observed suggestive evidence of a similar event in this trio, and performed Sanger sequencing to confirm the 21-bp duplication in the proband and affected father. The variant is absent from population frequency databases (gnomAD). Functional studies of the polyalanine repeat in exon 1 have shown that an increase of the Ala repeat above a certain length (22 Ala) is associated with a shift in the localization of Hoxd13 from nuclear to cytoplasmic, where it forms large amorphous aggregates (PMID: 15333588). We interpret the variant as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.0
Mutation Taster		=74/26	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs878854345; hg19: chr2-176957822;