CYB5D2

cytochrome b5 domain containing 2, the group of Membrane associated progesterone receptor family

Basic information

Region (hg38): 17:4143168-4187310

Links

ENSG00000167740 ∙ NCBI:124936 ∙ ∙ HGNC:28471 ∙ Uniprot:Q8WUJ1 ∙ 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 CYB5D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYB5D2 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in CYB5D2

This is a list of pathogenic ClinVar variants found in the CYB5D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4143774-C-T		not specified	Uncertain significance (Jun 03, 2022)
17-4143808-C-T		not specified	Uncertain significance (Mar 14, 2023)
17-4143811-C-T		not specified	Uncertain significance (May 31, 2023)
17-4143843-G-A		not specified	Likely benign (Oct 12, 2022)
17-4143909-G-C		not specified	Uncertain significance (Oct 10, 2023)
17-4143912-C-T		not specified	Uncertain significance (Jun 03, 2024)
17-4143940-G-T		not specified	Uncertain significance (Jul 09, 2021)
17-4143991-A-G		not specified	Uncertain significance (Feb 27, 2023)
17-4149909-C-T		not specified	Uncertain significance (Nov 04, 2022)
17-4149914-G-C		not specified	Uncertain significance (Jun 09, 2022)
17-4149953-G-T		not specified	Uncertain significance (Jul 31, 2024)
17-4149961-C-A		not specified	Uncertain significance (Jun 29, 2023)
17-4149961-C-G		not specified	Uncertain significance (Mar 28, 2024)
17-4149972-C-A		not specified	Uncertain significance (Jun 05, 2024)
17-4150028-G-T		not specified	Uncertain significance (Dec 15, 2022)
17-4154674-G-C		not specified	Uncertain significance (Feb 10, 2023)
17-4154689-G-A		not specified	Uncertain significance (Sep 30, 2024)
17-4154719-C-T		not specified	Uncertain significance (Sep 29, 2023)
17-4154733-G-A		not specified	Uncertain significance (May 05, 2023)
17-4154768-C-A		not specified	Uncertain significance (Feb 27, 2023)
17-4154794-C-T		not specified	Uncertain significance (Feb 14, 2023)
17-4154812-C-T		not specified	Uncertain significance (Nov 11, 2024)
17-4156894-G-A		not specified	Uncertain significance (Oct 23, 2024)
17-4156961-C-T		not specified	Uncertain significance (May 09, 2024)
17-4156963-C-A		not specified	Uncertain significance (Apr 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYB5D2	protein_coding	protein_coding	ENST00000301391	4	44144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000443	0.407	125642	1	105	125748	0.000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.606	193	171	1.13	0.00000969	1679
Missense in Polyphen		48	45.801	1.048		453
Synonymous	-0.955	88	77.3	1.14	0.00000503	568
Loss of Function	0.475	9	10.7	0.843	5.41e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000708	0.000707
Finnish	0.00148	0.00148
European (Non-Finnish)	0.000259	0.000255
Middle Eastern	0.000708	0.000707
South Asian	0.000687	0.000686
Other	0.000985	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Heme-binding protein which promotes neuronal but not astrocyte differentiation. {ECO:0000250}.

Recessive Scores

• pRec: 0.215

Intolerance Scores

• loftool: 0.508
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.0988
• hipred: N
• hipred_score: 0.197
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.278

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyb5d2
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of neuron differentiation
• Cellular component: extracellular region
• Molecular function: heme binding