CNBD2

cyclic nucleotide binding domain containing 2

Basic information

Region (hg38): 20:35954564-36030700

Previous symbols: [ "C20orf152", "CNMPD1" ]

Links

ENSG00000149646 ∙ NCBI:140894 ∙ ∙ HGNC:16145 ∙ Uniprot:Q96M20 ∙ 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 CNBD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNBD2 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			44	5		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	5	0

Variants in CNBD2

This is a list of pathogenic ClinVar variants found in the CNBD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35968775-A-T		not specified	Uncertain significance (Jun 29, 2023)
20-35968784-T-C		not specified	Likely benign (Oct 19, 2021)
20-35972693-G-T		not specified	Uncertain significance (Mar 20, 2023)
20-35972702-G-A		not specified	Uncertain significance (Sep 26, 2023)
20-35975958-C-G		not specified	Uncertain significance (Mar 16, 2022)
20-35975965-G-T		not specified	Uncertain significance (Jun 02, 2023)
20-35980486-A-T		not specified	Uncertain significance (Jan 09, 2024)
20-35980501-C-A		not specified	Uncertain significance (Sep 26, 2023)
20-35980534-G-A		not specified	Uncertain significance (Jun 16, 2023)
20-35980567-C-T		not specified	Uncertain significance (Jun 16, 2023)
20-35980576-G-T		not specified	Likely benign (Jun 02, 2023)
20-35980613-G-A		not specified	Uncertain significance (May 27, 2022)
20-35983989-C-T		not specified	Uncertain significance (Nov 08, 2022)
20-35983990-G-A		not specified	Uncertain significance (Dec 15, 2022)
20-35983996-G-A		not specified	Uncertain significance (Jul 20, 2021)
20-35984023-G-A		not specified	Uncertain significance (Jan 30, 2024)
20-35984098-A-T		not specified	Uncertain significance (Mar 25, 2024)
20-35984107-C-T		not specified	Uncertain significance (Sep 22, 2022)
20-35984669-G-A		not specified	Uncertain significance (Jan 18, 2023)
20-35984676-T-C		not specified	Uncertain significance (May 23, 2023)
20-35984705-C-T		not specified	Uncertain significance (Jan 30, 2024)
20-35984746-G-T		not specified	Uncertain significance (Jan 10, 2023)
20-35987511-C-A		not specified	Uncertain significance (Aug 01, 2022)
20-35987521-G-C		not specified	Uncertain significance (Oct 02, 2023)
20-35995054-T-C		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNBD2	protein_coding	protein_coding	ENST00000349339	12	62111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.84e-17	0.0203	125637	0	111	125748	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.192	310	320	0.970	0.0000175	3800
Missense in Polyphen		82	76.751	1.0684		897
Synonymous	0.327	114	119	0.962	0.00000649	1037
Loss of Function	0.501	27	30.0	0.901	0.00000154	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00239	0.00239
Ashkenazi Jewish	0.00	0.00
East Asian	0.00110	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.00110	0.000925
South Asian	0.000549	0.000523
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for male fertility. Plays an important role in spermatogenesis and regulates sperm motility by controlling the development of the flagellar bending of sperm. {ECO:0000250|UniProtKB:Q9D5U8}.

Intolerance Scores

• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.145
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnbd2
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: spermatogenesis
• Cellular component: cytosol
• Molecular function: cAMP binding