HOXD1

homeobox D1, the group of HOXL subclass homeoboxes|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:176188668-176190907

Previous symbols: [ "HOX4", "HOX4G" ]

Links

ENSG00000128645 ∙ NCBI:3231 ∙ OMIM:142987 ∙ HGNC:5132 ∙ Uniprot:Q9GZZ0 ∙ 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 HOXD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXD1 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			26			26
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in HOXD1

This is a list of pathogenic ClinVar variants found in the HOXD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-176188827-C-T		not specified	Uncertain significance (Aug 20, 2024)
2-176188860-T-C		not specified	Uncertain significance (Aug 20, 2024)
2-176188892-G-A		not specified	Uncertain significance (Oct 24, 2024)
2-176188911-T-C		not specified	Uncertain significance (Oct 19, 2024)
2-176188992-C-T		not specified	Uncertain significance (May 01, 2023)
2-176189063-G-A		not specified	Uncertain significance (May 06, 2022)
2-176189088-C-A		not specified	Uncertain significance (Oct 20, 2023)
2-176189104-T-TG			Uncertain significance (Oct 01, 2019)
2-176189129-G-T		not specified	Uncertain significance (Mar 06, 2023)
2-176189136-G-A		not specified	Uncertain significance (Apr 19, 2024)
2-176189136-G-T		not specified	Uncertain significance (Jun 02, 2023)
2-176189148-A-G		not specified	Uncertain significance (Jul 07, 2022)
2-176189152-C-G		not specified	Uncertain significance (May 26, 2024)
2-176189183-G-A		not specified	Uncertain significance (Aug 13, 2021)
2-176189243-C-T		not specified	Uncertain significance (Dec 14, 2023)
2-176189253-A-G		not specified	Uncertain significance (Jul 20, 2022)
2-176189259-A-C		not specified	Uncertain significance (Sep 16, 2021)
2-176189273-G-C		not specified	Uncertain significance (Apr 12, 2023)
2-176189816-G-T		not specified	Uncertain significance (Nov 15, 2024)
2-176189825-G-T		not specified	Uncertain significance (Dec 27, 2023)
2-176189907-A-G		not specified	Uncertain significance (Oct 06, 2021)
2-176189911-G-C		not specified	Uncertain significance (Feb 27, 2024)
2-176189954-C-T		not specified	Uncertain significance (Nov 17, 2022)
2-176189957-C-G		not specified	Uncertain significance (Oct 21, 2021)
2-176190075-C-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXD1	protein_coding	protein_coding	ENST00000331462	2	2382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00318	0.836	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0362	173	172	1.01	0.00000780	2047
Missense in Polyphen		50	48.21	1.0371		606
Synonymous	0.128	78	79.4	0.982	0.00000384	719
Loss of Function	1.16	5	8.70	0.575	3.88e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000911	0.000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.00178	0.000870
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000124	0.000114
Middle Eastern	0.00178	0.000870
South Asian	0.000164	0.000163
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. Acts on the anterior body structures.
• Pathway: Activation of anterior HOX genes in hindbrain development during early embryogenesis (Consensus)

Recessive Scores

• pRec: 0.112

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.290

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.593

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxd1
• Phenotype: craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;sensory perception of pain;neuron differentiation;embryonic skeletal system development
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding