CYGB

cytoglobin

Basic information

Region (hg38): 17:76527356-76551175

Links

ENSG00000161544 ∙ NCBI:114757 ∙ OMIM:608759 ∙ HGNC:16505 ∙ Uniprot:Q8WWM9 ∙ 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 CYGB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYGB 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					2	2
missense			15	1		16
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	1	2

Variants in CYGB

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

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

Position	Type	Phenotype	Significance	ClinVar
17-76528584-C-T			Benign (Dec 31, 2019)
17-76528610-G-A		not specified	Uncertain significance (Dec 28, 2023)
17-76530983-T-C		not specified	Uncertain significance (Sep 20, 2023)
17-76531055-G-A		not specified	Uncertain significance (Dec 22, 2023)
17-76531078-G-A		not specified	Uncertain significance (Jun 10, 2022)
17-76531128-G-T			Benign (Aug 20, 2018)
17-76531142-T-A		not specified	Uncertain significance (Nov 06, 2023)
17-76531491-A-G		not specified	Uncertain significance (May 27, 2022)
17-76531516-C-T		not specified	Uncertain significance (Dec 04, 2023)
17-76531533-T-C		not specified	Uncertain significance (Dec 28, 2022)
17-76531558-C-T		not specified	Uncertain significance (Mar 17, 2023)
17-76531600-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-76531614-C-T		not specified	Uncertain significance (Aug 16, 2022)
17-76531631-A-T		not specified	Likely benign (Mar 14, 2024)
17-76537499-C-T		not specified	Uncertain significance (Jul 09, 2021)
17-76537508-C-A		not specified	Uncertain significance (Apr 26, 2023)
17-76537519-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-76537527-C-T		not specified	Uncertain significance (Mar 13, 2023)
17-76540048-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
17-76540060-T-C		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
17-76540143-T-C		Retinitis pigmentosa • Retinitis pigmentosa 36 • Retinal dystrophy	Pathogenic/Likely pathogenic (Oct 01, 2023)
17-76540146-G-A		Retinitis pigmentosa 36	Uncertain significance (Aug 04, 2023)
17-76540153-C-G			Likely benign (Jan 01, 2019)
17-76540154-C-G		Retinitis pigmentosa • Inborn genetic diseases	Uncertain significance (Nov 23, 2022)
17-76540156-T-G			Likely benign (Sep 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYGB	protein_coding	protein_coding	ENST00000293230	4	23820

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.102	0.868	125109	0	3	125112	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.846	91	117	0.780	0.00000676	1227
Missense in Polyphen		32	39.124	0.8179		426
Synonymous	0.618	46	51.7	0.891	0.00000344	372
Loss of Function	1.87	3	9.07	0.331	5.57e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000652	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.0000192	0.0000177
Middle Eastern	0.0000652	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a protective function during conditions of oxidative stress. May be involved in intracellular oxygen storage or transfer.
• Pathway: Metabolism of nitric oxide;eNOS activation;eNOS activation and regulation;Metabolism;Transport of small molecules;Intracellular oxygen transport (Consensus)

Recessive Scores

• pRec: 0.287

Intolerance Scores

• loftool: 0.149
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.582
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.316

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cygb
• Phenotype: liver/biliary system phenotype; neoplasm; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to hypoxia;response to oxidative stress;negative regulation of fibroblast migration;oxygen transport;fatty acid oxidation;negative regulation of collagen biosynthetic process;regulation of nitric-oxide synthase activity;cellular oxidant detoxification;negative regulation of hepatic stellate cell activation
• Cellular component: cytosol;nuclear speck;neuron projection;neuronal cell body
• Molecular function: catalase activity;peroxidase activity;oxygen carrier activity;iron ion binding;protein binding;nitric oxide dioxygenase activity;oxygen binding;heme binding;fatty acid peroxidase activity