CNBD1

cyclic nucleotide binding domain containing 1

Basic information

Region (hg38): 8:86866414-87615219

Links

ENSG00000176571 ∙ NCBI:168975 ∙ ∙ HGNC:26663 ∙ Uniprot:Q8NA66 ∙ 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 CNBD1 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNBD1 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in CNBD1

This is a list of pathogenic ClinVar variants found in the CNBD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-86866557-C-T		not specified	Uncertain significance (Aug 17, 2022)
8-86905083-G-A		not specified	Uncertain significance (Aug 30, 2022)
8-86905144-C-G		not specified	Uncertain significance (Jul 10, 2023)
8-86939603-A-G		not specified	Uncertain significance (Mar 28, 2023)
8-86939714-A-G		not specified	Uncertain significance (Oct 27, 2021)
8-87206007-C-T		not specified	Uncertain significance (Dec 27, 2023)
8-87206130-G-A		not specified	Uncertain significance (Jul 25, 2023)
8-87236946-T-C		not specified	Uncertain significance (Dec 13, 2023)
8-87237023-A-G		not specified	Uncertain significance (Jan 31, 2022)
8-87237041-A-G		not specified	Uncertain significance (Jun 29, 2023)
8-87237048-T-C		not specified	Uncertain significance (Jan 23, 2024)
8-87237064-C-A		not specified	Likely benign (Oct 26, 2021)
8-87284694-C-T		not specified	Uncertain significance (Dec 06, 2022)
8-87284697-T-C		not specified	Uncertain significance (Dec 20, 2023)
8-87286546-T-C		not specified	Uncertain significance (Sep 27, 2021)
8-87286581-C-T		not specified	Uncertain significance (Jan 03, 2022)
8-87286615-T-C		not specified	Uncertain significance (Jun 12, 2023)
8-87286626-G-C		not specified	Uncertain significance (Dec 16, 2023)
8-87286627-A-T		not specified	Uncertain significance (Jan 23, 2024)
8-87351766-G-A		not specified	Uncertain significance (Sep 23, 2023)
8-87351781-G-T		not specified	Uncertain significance (Aug 11, 2022)
8-87353651-C-T		not specified	Uncertain significance (Sep 16, 2021)
8-87353675-G-A		not specified	Uncertain significance (Dec 15, 2022)
8-87353690-G-C		not specified	Uncertain significance (Aug 19, 2021)
8-87353724-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNBD1	protein_coding	protein_coding	ENST00000518476	11	748778

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.49e-18	0.000806	124573	0	44	124617	0.000177

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.33	255	202	1.26	0.00000973	2866
Missense in Polyphen		61	48.898	1.2475		730
Synonymous	0.804	62	70.6	0.878	0.00000389	753
Loss of Function	-0.917	24	19.6	1.22	8.93e-7	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000909	0.000891
Ashkenazi Jewish	0.00	0.00
East Asian	0.000463	0.000389
Finnish	0.0000470	0.0000464
European (Non-Finnish)	0.0000549	0.0000531
Middle Eastern	0.000463	0.000389
South Asian	0.000302	0.000294
Other	0.000194	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.536
• rvis_EVS: 0.82
• rvis_percentile_EVS: 88.02

Haploinsufficiency Scores

• pHI: 0.0855
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnbd1
• Phenotype: homeostasis/metabolism phenotype