CYB5D1

cytochrome b5 domain containing 1

Basic information

Region (hg38): 17:7857746-7862282

Links

ENSG00000182224 ∙ NCBI:124637 ∙ ∙ HGNC:26516 ∙ Uniprot:Q6P9G0 ∙ 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 CYB5D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYB5D1 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in CYB5D1

This is a list of pathogenic ClinVar variants found in the CYB5D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7858141-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-7858145-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-7858199-C-G		not specified	Uncertain significance (Dec 19, 2022)
17-7858225-C-T		not specified	Uncertain significance (Oct 06, 2021)
17-7858439-G-A		not specified	Uncertain significance (May 21, 2024)
17-7858450-A-G		not specified	Uncertain significance (Aug 04, 2023)
17-7858460-T-C		not specified	Uncertain significance (Oct 09, 2024)
17-7858475-G-A		not specified	Likely benign (Jan 26, 2022)
17-7858710-C-G		not specified	Uncertain significance (Dec 28, 2022)
17-7858716-T-G		not specified	Uncertain significance (Jan 30, 2024)
17-7858775-G-A		not specified	Uncertain significance (Dec 05, 2024)
17-7858784-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-7859418-C-T		not specified	Uncertain significance (Aug 02, 2021)
17-7859431-A-G		not specified	Uncertain significance (Aug 10, 2021)
17-7859451-T-C		not specified	Uncertain significance (Aug 08, 2023)
17-7859486-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-7859487-G-C		not specified	Uncertain significance (May 09, 2023)
17-7859491-T-C		not specified	Uncertain significance (Jun 18, 2024)
17-7859529-G-C		not specified	Uncertain significance (Sep 09, 2021)
17-7859539-A-G		not specified	Uncertain significance (Apr 13, 2023)
17-7859595-G-C		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYB5D1	protein_coding	protein_coding	ENST00000332439	4	4537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.90e-10	0.0280	125681	0	67	125748	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.863	107	135	0.791	0.00000701	1476
Missense in Polyphen		46	52.831	0.8707		556
Synonymous	0.100	58	59.0	0.983	0.00000323	457
Loss of Function	-0.714	13	10.5	1.24	4.58e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000950	0.000949
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000275	0.000273
Middle Eastern	0.0000544	0.0000544
South Asian	0.000102	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.650
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.329
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.809

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyb5d1
• Phenotype: skeleton phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Molecular function: metal ion binding