HOXD8

homeobox D8, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 2:176129694-176132695

Previous symbols: [ "HOX4", "HOX4E" ]

Links

ENSG00000175879 ∙ NCBI:3234 ∙ OMIM:142985 ∙ HGNC:5139 ∙ Uniprot:P13378 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HOXD8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXD8 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			41			41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	0	0

Variants in HOXD8

This is a list of pathogenic ClinVar variants found in the HOXD8 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-176130397-T-C		not specified	Uncertain significance (Jun 29, 2022)
2-176130431-C-A		not specified	Uncertain significance (Sep 27, 2024)
2-176130434-C-G		not specified	Uncertain significance (Aug 12, 2024)
2-176130454-A-C		not specified	Uncertain significance (Sep 16, 2021)
2-176130484-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-176130493-C-T		not specified	Uncertain significance (Mar 23, 2023)
2-176130496-C-A		not specified	Uncertain significance (Dec 04, 2024)
2-176130496-C-G		not specified	Uncertain significance (Oct 26, 2022)
2-176130496-C-T		not specified	Uncertain significance (Jul 13, 2021)
2-176130498-C-G		not specified	Uncertain significance (Dec 21, 2024)
2-176130505-G-T		not specified	Uncertain significance (Aug 08, 2022)
2-176130509-C-A		not specified	Uncertain significance (Aug 02, 2021)
2-176130518-T-C		not specified	Uncertain significance (Nov 03, 2024)
2-176130535-A-C		not specified	Uncertain significance (Dec 14, 2021)
2-176130570-G-A		HOXD8-related disorder	Likely benign (Nov 05, 2020)
2-176130577-C-T		not specified	Uncertain significance (Jan 29, 2024)
2-176130578-A-C		not specified	Uncertain significance (Oct 10, 2023)
2-176130579-C-A		not specified	Uncertain significance (Jun 13, 2022)
2-176130586-C-T		not specified	Uncertain significance (Mar 25, 2024)
2-176130587-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-176130590-C-G		not specified	Uncertain significance (Jun 22, 2021)
2-176130601-T-A		not specified	Uncertain significance (Sep 26, 2024)
2-176130616-G-A		not specified	Uncertain significance (Mar 15, 2024)
2-176130658-G-T		not specified	Uncertain significance (Jul 02, 2024)
2-176130664-A-C		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXD8	protein_coding	protein_coding	ENST00000313173	2	3002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.105	0.866	125730	0	15	125745	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.42	182	136	1.34	0.00000631	1850
Missense in Polyphen		52	49.994	1.0401		713
Synonymous	-2.28	80	57.9	1.38	0.00000291	570
Loss of Function	1.88	3	9.15	0.328	3.99e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000208	0.000188
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.000112	0.000109
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase (Consensus)

Recessive Scores

• pRec: 0.107

Haploinsufficiency Scores

• pHI: 0.204
• hipred: Y
• hipred_score: 0.669
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.709

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hoxd8
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;anterior/posterior axis specification, embryo;positive regulation of transcription by RNA polymerase II;skeletal system morphogenesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific