CYB5R2

cytochrome b5 reductase 2

Basic information

Region (hg38): 11:7665100-7677222

Links

ENSG00000166394 ∙ NCBI:51700 ∙ OMIM:608342 ∙ HGNC:24376 ∙ Uniprot:Q6BCY4 ∙ 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 CYB5R2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYB5R2 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in CYB5R2

This is a list of pathogenic ClinVar variants found in the CYB5R2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-7665389-C-A		not specified	Uncertain significance (Nov 12, 2024)
11-7665394-C-T		not specified	Uncertain significance (Dec 10, 2024)
11-7665427-G-A		not specified	Uncertain significance (Jun 17, 2024)
11-7665439-G-C		not specified	Uncertain significance (Oct 06, 2024)
11-7665448-G-C		not specified	Uncertain significance (Aug 11, 2022)
11-7665453-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-7665483-G-A		not specified	Uncertain significance (Oct 06, 2021)
11-7665496-G-C		not specified	Uncertain significance (Feb 13, 2023)
11-7665502-C-G		not specified	Uncertain significance (Nov 25, 2024)
11-7665507-A-T		not specified	Uncertain significance (Dec 31, 2023)
11-7665517-C-T		not specified	Uncertain significance (Sep 14, 2022)
11-7665519-G-A		not specified	Uncertain significance (Nov 30, 2022)
11-7665542-C-G		not specified	Uncertain significance (Sep 22, 2023)
11-7666454-T-C		not specified	Likely benign (Mar 18, 2024)
11-7666493-C-T		not specified	Uncertain significance (Jan 31, 2022)
11-7666507-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-7666528-C-T		not specified	Uncertain significance (Jul 07, 2022)
11-7666532-C-G		not specified	Uncertain significance (May 30, 2024)
11-7667760-T-C		not specified	Uncertain significance (Oct 07, 2024)
11-7667771-T-C		not specified	Uncertain significance (Aug 02, 2023)
11-7668484-C-T		not specified	Uncertain significance (May 22, 2023)
11-7668498-C-T		not specified	Uncertain significance (Nov 08, 2024)
11-7668535-T-C		not specified	Uncertain significance (Mar 17, 2023)
11-7668536-C-G		not specified	Uncertain significance (Oct 08, 2024)
11-7669226-G-A		not specified	Uncertain significance (Apr 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYB5R2	protein_coding	protein_coding	ENST00000533558	8	12123

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.82e-10	0.0736	125630	0	118	125748	0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.28	204	159	1.29	0.00000862	1814
Missense in Polyphen		67	61.929	1.0819		733
Synonymous	-1.83	81	62.6	1.29	0.00000377	518
Loss of Function	-0.0436	14	13.8	1.01	6.50e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000858	0.000858
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000680	0.000677
Middle Eastern	0.000109	0.000109
South Asian	0.000654	0.000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: NADH-cytochrome b5 reductases are involved in desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction (By similarity). Responsible for NADH-dependent lucigenin chemiluminescence in spermatozoa by reducing both lucigenin and 2-[4-iodophenyl]-3-[4-nitrophenyl]-5-[2,4- disulfophenyl]-2H tetrazolium monosodium salt (WST-1). {ECO:0000250, ECO:0000269|PubMed:15858218}.
• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Oxidation by Cytochrome P450;O2/CO2 exchange in erythrocytes;Transport of small molecules;Erythrocytes take up carbon dioxide and release oxygen (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.250
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.21

Haploinsufficiency Scores

• pHI: 0.231
• hipred: N
• hipred_score: 0.197
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.474

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyb5r2

Gene ontology

• Biological process: bicarbonate transport;sterol biosynthetic process;oxidation-reduction process
• Cellular component: nucleus;endoplasmic reticulum membrane;membrane
• Molecular function: cytochrome-b5 reductase activity, acting on NAD(P)H;protein binding;FAD binding