HMOX2

heme oxygenase 2

Basic information

Region (hg38): 16:4474690-4510347

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.

• not_specified (43 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. These statistics are base on transcript: NM_000002134.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			43	3		46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4			4
Total	0	0	47	3	1

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
		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

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

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