HMOX2

heme oxygenase 2

Basic information

Region (hg38): 16:4474689-4510347

Links

ENSG00000103415 ∙ NCBI:3163 ∙ OMIM:141251 ∙ HGNC:5014 ∙ Uniprot:P30519 ∙ 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 HMOX2 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMOX2 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					1	1
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	1

Variants in HMOX2

This is a list of pathogenic ClinVar variants found in the HMOX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4505561-G-A		not specified	Uncertain significance (Jun 28, 2022)
16-4506947-C-T		not specified	Uncertain significance (Feb 23, 2023)
16-4506948-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-4507002-A-G		not specified	Uncertain significance (Dec 21, 2021)
16-4507747-C-G		not specified	Uncertain significance (Dec 26, 2023)
16-4507817-G-A			Benign (Jun 10, 2018)
16-4507831-C-T		not specified	Uncertain significance (Feb 27, 2024)
16-4507894-A-T		not specified	Uncertain significance (May 31, 2023)
16-4507903-A-G		not specified	Likely benign (Jan 04, 2022)
16-4507974-C-T		not specified	Uncertain significance (Oct 26, 2021)
16-4507986-G-A		not specified	Uncertain significance (Nov 10, 2022)
16-4507993-C-T		not specified	Uncertain significance (May 23, 2023)
16-4508015-G-C		not specified	Uncertain significance (Jan 26, 2023)
16-4509412-A-T		not specified	Uncertain significance (Dec 14, 2021)
16-4509414-A-G		not specified	Uncertain significance (Jan 24, 2024)
16-4509418-A-C		not specified	Uncertain significance (Sep 21, 2023)
16-4509433-G-C		not specified	Uncertain significance (Nov 10, 2022)
16-4509511-C-T		not specified	Uncertain significance (Dec 03, 2021)
16-4509526-G-A		not specified	Likely benign (Dec 06, 2023)
16-4509533-A-G		not specified	Uncertain significance (Aug 19, 2023)
16-4509650-G-C		not specified	Uncertain significance (May 27, 2022)
16-4509749-A-G		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMOX2	protein_coding	protein_coding	ENST00000570646	5	35658

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000262	0.936	125560	2	185	125747	0.000744

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	182	186	0.977	0.0000107	2081
Missense in Polyphen		43	53.506	0.80364		620
Synonymous	-0.190	78	75.9	1.03	0.00000466	593
Loss of Function	1.67	8	14.9	0.535	8.02e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00154	0.00144
Ashkenazi Jewish	0.0131	0.0130
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000101	0.0000980
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed. Heme oxygenase 2 could be implicated in the production of carbon monoxide in brain where it could act as a neurotransmitter.
• Pathway: Porphyrin and chlorophyll metabolism - Homo sapiens (human);Mineral absorption - Homo sapiens (human);Neutrophil degranulation;oxidative stress induced gene expression via nrf2;heme degradation;Heme degradation;Metabolism of porphyrins;Innate Immune System;Immune System;Metabolism;Transport of small molecules;Iron uptake and transport (Consensus)

Recessive Scores

• pRec: 0.626

Intolerance Scores

• loftool: 0.879
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.0905
• hipred: N
• hipred_score: 0.350
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmox2
• 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); homeostasis/metabolism phenotype; muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; digestive/alimentary 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)

Gene ontology

• Biological process: response to hypoxia;heme oxidation;cellular iron ion homeostasis;response to oxidative stress;heme catabolic process;neutrophil degranulation;iron ion homeostasis
• Cellular component: endoplasmic reticulum membrane;plasma membrane;membrane;specific granule membrane
• Molecular function: heme oxygenase (decyclizing) activity;protein binding;heme binding;metal ion binding