HMX3

H6 family homeobox 3, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 10:123135969-123139423

Links

ENSG00000188620 ∙ NCBI:340784 ∙ OMIM:613380 ∙ HGNC:5019 ∙ Uniprot:A6NHT5 ∙ 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 HMX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMX3 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in HMX3

This is a list of pathogenic ClinVar variants found in the HMX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-123136186-C-T		not specified	Uncertain significance (Dec 18, 2023)
10-123136187-C-G			Uncertain significance (Feb 15, 2021)
10-123136193-C-T		not specified	Uncertain significance (Dec 21, 2023)
10-123136207-C-T		not specified	Uncertain significance (Jun 30, 2022)
10-123136231-G-C		not specified	Uncertain significance (Jan 19, 2022)
10-123136262-C-T		not specified	Uncertain significance (Aug 30, 2021)
10-123136285-G-A		not specified	Uncertain significance (Jul 21, 2021)
10-123136327-T-G		not specified	Uncertain significance (Sep 22, 2023)
10-123136346-C-T		not specified	Uncertain significance (Apr 22, 2022)
10-123136381-G-C		not specified	Uncertain significance (Jan 30, 2024)
10-123136435-C-A		not specified	Uncertain significance (Jan 04, 2024)
10-123136441-C-G		not specified	Uncertain significance (Apr 12, 2024)
10-123137109-G-T		not specified	Uncertain significance (Jun 17, 2024)
10-123137153-G-A		not specified	Uncertain significance (Jun 29, 2022)
10-123137166-A-G		not specified	Uncertain significance (May 03, 2023)
10-123137192-G-C		not specified	Uncertain significance (Feb 17, 2022)
10-123137195-A-T		not specified	Uncertain significance (May 04, 2023)
10-123137196-G-C		not specified	Uncertain significance (Jul 26, 2022)
10-123137261-G-C		not specified	Uncertain significance (Mar 23, 2022)
10-123137276-C-T		not specified	Uncertain significance (Dec 15, 2022)
10-123137307-A-G		not specified	Uncertain significance (Aug 12, 2021)
10-123137343-A-C		not specified	Uncertain significance (Jul 14, 2021)
10-123137363-C-A		not specified	Uncertain significance (Sep 27, 2021)
10-123137531-G-C		not specified	Uncertain significance (Sep 14, 2021)
10-123137532-C-T		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMX3	protein_coding	protein_coding	ENST00000357878	2	1780

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.920	0.0796	124117	0	1	124118	0.00000403

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.908	142	176	0.807	0.00000793	2196
Missense in Polyphen		27	55.406	0.48731		626
Synonymous	-1.12	95	82.1	1.16	0.00000398	772
Loss of Function	2.64	0	8.09	0.00	3.44e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000893	0.00000893
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor involved in specification of neuronal cell types and which is required for inner ear and hypothalamus development. Binds to the 5'-CAAGTG-3' core sequence. Controls semicircular canal formation in the inner ear. Also required for hypothalamic/pituitary axis of the CNS (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.134

Haploinsufficiency Scores

• pHI: 0.328
• hipred: Y
• hipred_score: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmx3
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; muscle phenotype; 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); hearing/vestibular/ear phenotype; reproductive system 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype

Zebrafish Information Network

• Gene name: hmx3a
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: fused with

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;brain development;embryo implantation;cell differentiation;inner ear morphogenesis;neuromuscular process controlling balance;maternal process involved in female pregnancy
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific