HMX2

H6 family homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 10:123148136-123150672

Links

ENSG00000188816 ∙ NCBI:3167 ∙ OMIM:600647 ∙ HGNC:5018 ∙ Uniprot:A2RU54 ∙ 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 HMX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMX2 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
missense			24		1	25
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	2	1

Variants in HMX2

This is a list of pathogenic ClinVar variants found in the HMX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-123148529-T-A		not specified	Uncertain significance (Feb 23, 2023)
10-123148611-C-T		not specified	Uncertain significance (Oct 10, 2023)
10-123148629-T-C		not specified	Uncertain significance (Nov 15, 2024)
10-123148643-C-G		not specified	Uncertain significance (Nov 12, 2024)
10-123149569-G-A		High myopia	Uncertain significance (Dec 17, 2018)
10-123149576-C-G		not specified	Uncertain significance (Jan 23, 2024)
10-123149588-G-T		not specified	Uncertain significance (Dec 20, 2021)
10-123149604-C-A			Likely benign (Jun 13, 2018)
10-123149614-C-G		not specified	Uncertain significance (Jan 29, 2025)
10-123149643-G-A		HMX2-related disorder	Likely benign (Jul 12, 2019)
10-123149650-A-G		not specified	Uncertain significance (Oct 20, 2023)
10-123149705-G-A		not specified	Uncertain significance (Feb 26, 2025)
10-123149734-G-A		not specified	Uncertain significance (May 15, 2024)
10-123149740-G-T		not specified	Uncertain significance (Dec 21, 2023)
10-123149756-C-T		not specified	Uncertain significance (Jan 08, 2024)
10-123149789-A-G		not specified	Uncertain significance (Sep 08, 2024)
10-123149810-T-G		not specified	Uncertain significance (Jun 18, 2024)
10-123149852-C-G		not specified	Uncertain significance (Apr 13, 2023)
10-123149872-A-G		not specified	Uncertain significance (Apr 10, 2023)
10-123149880-A-G			Likely benign (Jun 13, 2018)
10-123149902-C-T		not specified	Uncertain significance (Feb 27, 2023)
10-123149913-G-C		not specified	Uncertain significance (Feb 01, 2023)
10-123149945-C-T		not specified	Uncertain significance (Nov 12, 2024)
10-123149949-C-G		not specified	Uncertain significance (May 23, 2023)
10-123149959-G-C		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMX2	protein_coding	protein_coding	ENST00000339992	2	2551

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000499	0.445	125495	0	23	125518	0.0000916

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0851	156	153	1.02	0.00000696	1715
Missense in Polyphen		52	58.184	0.89372		634
Synonymous	-1.75	93	73.9	1.26	0.00000350	580
Loss of Function	0.356	7	8.09	0.865	3.47e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000444	0.000425
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000833	0.0000794
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor involved in specification of neuronal cell types and which is required for inner ear and hypothalamus development. {ECO:0000250}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.219
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.708
• hipred: Y
• hipred_score: 0.538
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.566

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmx2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hearing/vestibular/ear 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)

Zebrafish Information Network

• Gene name: hmx2
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: fused with

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;brain development;positive regulation of cell population proliferation;cell differentiation;inner ear morphogenesis;positive regulation of mRNA splicing, via spliceosome
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding