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.

not_specified (38 variants)
not_provided (3 variants)
High_myopia (1 variants)
HMX2-related_disorder (1 variants)

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. These statistics are base on transcript: NM_000005519.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			38 clinvar		1 clinvar	39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	39	3	1

Loading clinvar variants...

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