CDADC1

cytidine and dCMP deaminase domain containing 1

Basic information

Region (hg38): 13:49247925-49293485

Links

ENSG00000102543 ∙ NCBI:81602 ∙ OMIM:618997 ∙ HGNC:20299 ∙ Uniprot:Q9BWV3 ∙ 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 CDADC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDADC1 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in CDADC1

This is a list of pathogenic ClinVar variants found in the CDADC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-49248876-A-G		not specified	Uncertain significance (Nov 09, 2023)
13-49259427-C-A		not specified	Likely benign (Jun 23, 2023)
13-49259449-G-A		not specified	Uncertain significance (Aug 09, 2021)
13-49259515-T-G		not specified	Uncertain significance (Nov 10, 2024)
13-49267571-A-G		not specified	Uncertain significance (Aug 02, 2021)
13-49267654-A-G		not specified	Uncertain significance (Aug 07, 2024)
13-49267733-C-A		not specified	Uncertain significance (Oct 05, 2022)
13-49267750-T-C		not specified	Uncertain significance (Jul 27, 2024)
13-49267775-A-G		not specified	Uncertain significance (Oct 25, 2022)
13-49267806-A-C		not specified	Uncertain significance (Jan 30, 2024)
13-49267825-A-G		not specified	Uncertain significance (Apr 07, 2023)
13-49267878-G-T		not specified	Uncertain significance (Apr 23, 2024)
13-49267958-G-A		not specified	Uncertain significance (Apr 24, 2023)
13-49267997-G-A		not specified	Uncertain significance (Apr 19, 2023)
13-49268054-G-A		not specified	Uncertain significance (Jul 17, 2023)
13-49274333-G-C		not specified	Uncertain significance (Oct 22, 2021)
13-49280514-A-G		not specified	Uncertain significance (Sep 25, 2023)
13-49280608-A-C		not specified	Uncertain significance (Aug 12, 2021)
13-49280655-C-T		not specified	Uncertain significance (Nov 08, 2022)
13-49291722-C-T		not specified	Uncertain significance (Dec 27, 2023)
13-49291741-G-A		not specified	Uncertain significance (Jan 26, 2022)
13-49291746-G-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDADC1	protein_coding	protein_coding	ENST00000251108	10	45572

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.15e-10	0.499	125693	0	53	125746	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	202	270	0.748	0.0000129	3414
Missense in Polyphen		62	91.885	0.67475		1222
Synonymous	0.567	86	92.9	0.925	0.00000462	909
Loss of Function	1.18	18	24.3	0.742	0.00000117	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000731	0.000731
Ashkenazi Jewish	0.000116	0.0000992
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.00	0.00
South Asian	0.000265	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in testicular development and spermatogenesis. {ECO:0000269|PubMed:16955368}.

Intolerance Scores

• loftool: 0.386
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.5

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.301
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdadc1

Gene ontology

• Biological process: dUMP biosynthetic process;dTMP biosynthetic process;cytidine deamination;DNA cytosine deamination
• Cellular component: nucleus;cytoplasm
• Molecular function: cytidine deaminase activity;dCMP deaminase activity;zinc ion binding;protein homodimerization activity;importin-alpha family protein binding