CDPF1

cysteine rich DPF motif domain containing 1

Basic information

Region (hg38): 22:46244010-46250311

Previous symbols: [ "C22orf40" ]

Links

ENSG00000205643 ∙ NCBI:150383 ∙ ∙ HGNC:33710 ∙ Uniprot:Q6NVV7 ∙ 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 CDPF1 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDPF1 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			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in CDPF1

This is a list of pathogenic ClinVar variants found in the CDPF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-46245160-G-A		not specified	Uncertain significance (Aug 09, 2021)
22-46245190-C-T		not specified	Uncertain significance (Mar 07, 2024)
22-46245207-C-A		not specified	Uncertain significance (Dec 20, 2023)
22-46245216-T-G		not specified	Uncertain significance (Aug 28, 2023)
22-46247162-A-G		not specified	Uncertain significance (Sep 12, 2023)
22-46248175-A-C		not specified	Uncertain significance (Jan 23, 2023)
22-46248230-T-C		not specified	Likely benign (Mar 23, 2022)
22-46248263-G-A		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDPF1	protein_coding	protein_coding	ENST00000314567	3	6669

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000215	0.166	125715	0	21	125736	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0201	74	74.5	0.993	0.00000448	797
Missense in Polyphen		27	25.618	1.0539		314
Synonymous	-0.0324	32	31.8	1.01	0.00000206	236
Loss of Function	-0.888	6	4.07	1.48	1.70e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000399	0.000395
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.27

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.415

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	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cdpf1

Gene ontology

• Molecular function: protein binding