CNBD1

cyclic nucleotide binding domain containing 1

Basic information

Region (hg38): 8:86866415-87615219

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.

• not_specified (60 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. These statistics are base on transcript: NM_000173538.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			55	4		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	5	0

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