CYB5R1

cytochrome b5 reductase 1

Basic information

Region (hg38): 1:202961873-202967275

Previous symbols: [ "NQO3A2" ]

Links

ENSG00000159348 ∙ NCBI:51706 ∙ OMIM:608341 ∙ HGNC:13397 ∙ Uniprot:Q9UHQ9 ∙ 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 CYB5R1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYB5R1 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			15			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	15	0	0

Variants in CYB5R1

This is a list of pathogenic ClinVar variants found in the CYB5R1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-202962561-A-C		not specified	Uncertain significance (Sep 26, 2022)
1-202962598-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-202962630-T-G		not specified	Uncertain significance (Nov 13, 2024)
1-202962650-G-T		not specified	Uncertain significance (Sep 02, 2024)
1-202962651-T-C		not specified	Uncertain significance (Mar 07, 2024)
1-202962667-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-202963116-C-T		not specified	Uncertain significance (Mar 23, 2022)
1-202963117-G-A		not specified	Uncertain significance (Mar 29, 2022)
1-202963144-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-202963161-T-C		not specified	Uncertain significance (Dec 13, 2021)
1-202963665-A-G		not specified	Uncertain significance (Apr 07, 2023)
1-202963701-G-A		not specified	Uncertain significance (Sep 30, 2024)
1-202963722-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-202964644-G-A		not specified	Uncertain significance (Oct 01, 2024)
1-202965406-C-T		not specified	Uncertain significance (May 28, 2024)
1-202965499-A-G		not specified	Uncertain significance (Jan 23, 2023)
1-202965906-T-C		not specified	Uncertain significance (Nov 25, 2024)
1-202965984-A-G		not specified	Uncertain significance (Jun 18, 2021)
1-202966580-C-G		not specified	Uncertain significance (Jun 07, 2024)
1-202966587-T-G		not specified	Uncertain significance (Feb 07, 2023)
1-202966850-C-T		not specified	Uncertain significance (Apr 16, 2024)
1-202966865-G-C		not specified	Uncertain significance (Aug 17, 2022)
1-202966895-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-202967201-C-T		not specified	Uncertain significance (Sep 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYB5R1	protein_coding	protein_coding	ENST00000367249	9	5412

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.36e-9	0.206	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.510	155	174	0.891	0.00000945	1944
Missense in Polyphen		64	75.374	0.8491		864
Synonymous	-0.696	77	69.6	1.11	0.00000351	644
Loss of Function	0.470	14	16.0	0.873	9.23e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000540	0.000539
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000264	0.000246
Middle Eastern	0.000217	0.000217
South Asian	0.000196	0.000196
Other	0.000367	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. {ECO:0000250}.
• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Oxidation by Cytochrome P450;O2/CO2 exchange in erythrocytes;Transport of small molecules;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis;Erythrocytes take up carbon dioxide and release oxygen (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.367
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.352
• hipred: N
• hipred_score: 0.282
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyb5r1

Gene ontology

• Biological process: platelet degranulation;bicarbonate transport;sterol biosynthetic process;oxidation-reduction process
• Cellular component: mitochondrion;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane;platelet alpha granule membrane;extracellular exosome
• Molecular function: cytochrome-b5 reductase activity, acting on NAD(P)H;protein binding;FAD binding