HOXD11

homeobox D11, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 2:176104216-176109754

Previous symbols: [ "HOX4", "HOX4F" ]

Links

ENSG00000128713 ∙ NCBI:3237 ∙ OMIM:142986 ∙ HGNC:5134 ∙ Uniprot:P31277 ∙ 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 HOXD11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXD11 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				2	2	4
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	2

Variants in HOXD11

This is a list of pathogenic ClinVar variants found in the HOXD11 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-176107362-G-C		not specified	Uncertain significance (Feb 12, 2024)
2-176107370-C-G		not specified	Uncertain significance (May 05, 2022)
2-176107387-C-A		not specified	Uncertain significance (Jan 31, 2023)
2-176107450-C-G		not specified	Uncertain significance (Dec 19, 2022)
2-176107459-T-C		not specified	Uncertain significance (Jan 08, 2024)
2-176107505-C-A		not specified	Uncertain significance (Oct 05, 2021)
2-176107507-T-G		not specified	Uncertain significance (Jan 02, 2024)
2-176107554-G-C		not specified	Uncertain significance (Mar 29, 2024)
2-176107587-G-A		not specified	Uncertain significance (Jan 26, 2023)
2-176107588-G-A		not specified	Uncertain significance (Dec 20, 2022)
2-176107590-G-C		not specified	Uncertain significance (Mar 13, 2023)
2-176107614-G-T		not specified	Uncertain significance (Apr 12, 2024)
2-176107660-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-176107697-T-C			Likely benign (Feb 01, 2023)
2-176107728-A-T		not specified	Uncertain significance (Jul 26, 2022)
2-176107773-C-T		not specified	Uncertain significance (Jul 13, 2022)
2-176107794-G-C		not specified	Uncertain significance (Apr 08, 2024)
2-176107813-C-A		not specified	Uncertain significance (Jan 23, 2024)
2-176107853-C-A		not specified	Uncertain significance (Jan 26, 2022)
2-176107855-C-A		not specified	Uncertain significance (Jun 27, 2022)
2-176107968-G-A		not specified	Uncertain significance (Oct 12, 2022)
2-176107987-G-T		not specified	Uncertain significance (Jan 26, 2023)
2-176108013-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-176108025-C-A		not specified	Uncertain significance (Jul 14, 2022)
2-176108074-G-A		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXD11	protein_coding	protein_coding	ENST00000249504	2	5779

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00114	0.637	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.591	136	118	1.15	0.00000542	2126
Missense in Polyphen		60	61.415	0.97696		852
Synonymous	-1.53	65	51.1	1.27	0.00000244	712
Loss of Function	0.605	5	6.69	0.748	2.86e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000224	0.000214
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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.

Haploinsufficiency Scores

• pHI: 0.240
• hipred: Y
• hipred_score: 0.538
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxd11
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; skeleton phenotype; renal/urinary system phenotype; limbs/digits/tail phenotype; cellular phenotype

Gene ontology

• Biological process: branching involved in ureteric bud morphogenesis;regulation of transcription by RNA polymerase II;dorsal/ventral pattern formation
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding