CDV3

CDV3 homolog

Basic information

Region (hg38): 3:133573686-133590261

Links

ENSG00000091527 ∙ NCBI:55573 ∙ OMIM:618789 ∙ HGNC:26928 ∙ Uniprot:Q9UKY7 ∙ 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 CDV3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDV3 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			16			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	16	0	0

Variants in CDV3

This is a list of pathogenic ClinVar variants found in the CDV3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-133574093-G-A		not specified	Uncertain significance (Feb 07, 2023)
3-133574148-C-T		not specified	Uncertain significance (Mar 01, 2024)
3-133574195-G-A		not specified	Uncertain significance (Mar 18, 2024)
3-133574199-C-T		not specified	Uncertain significance (Feb 01, 2023)
3-133574217-C-T		not specified	Uncertain significance (Apr 04, 2023)
3-133575072-G-A		not specified	Uncertain significance (Jun 09, 2022)
3-133584017-A-C		not specified	Uncertain significance (Mar 20, 2024)
3-133584033-A-G		not specified	Uncertain significance (Aug 08, 2022)
3-133584055-G-T		not specified	Uncertain significance (Nov 22, 2022)
3-133584078-G-A		not specified	Uncertain significance (Mar 11, 2024)
3-133584130-C-T		not specified	Uncertain significance (Oct 05, 2021)
3-133586586-A-T		not specified	Uncertain significance (Feb 16, 2023)
3-133587940-A-G		not specified	Uncertain significance (Mar 16, 2022)
3-133587961-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-133587966-A-C		not specified	Uncertain significance (Jul 26, 2021)
3-133587967-A-T		not specified	Uncertain significance (Jun 28, 2023)
3-133587978-A-C		not specified	Uncertain significance (Oct 03, 2022)
3-133588009-T-G		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDV3	protein_coding	protein_coding	ENST00000264993	5	16532

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.768	0.230	125685	0	14	125699	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.765	85	107	0.792	0.00000494	1673
Missense in Polyphen		26	40.018	0.64971		604
Synonymous	0.783	31	37.1	0.836	0.00000180	495
Loss of Function	2.50	1	9.18	0.109	3.87e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Fibroblast growth factor-1;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.0676

Intolerance Scores

• loftool: 0.195
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.0799
• hipred: N
• hipred_score: 0.318
• ghis: 0.666

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdv3

Gene ontology

• Biological process: cell population proliferation
• Cellular component: cytosol;plasma membrane
• Molecular function: molecular_function