CDCP2

CUB domain containing protein 2

Basic information

Region (hg38): 1:54132686-54153770

Links

ENSG00000157211 ∙ NCBI:200008 ∙ OMIM:612320 ∙ HGNC:27297 ∙ Uniprot:Q5VXM1 ∙ 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 CDCP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDCP2 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			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	3		6
Total	0	0	34	3	0

Variants in CDCP2

This is a list of pathogenic ClinVar variants found in the CDCP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-54139569-G-A		not specified	Uncertain significance (May 06, 2024)
1-54139573-C-T		not specified	Likely benign (May 03, 2023)
1-54139578-A-G		not specified	Likely benign (May 18, 2022)
1-54139585-G-C		not specified	Uncertain significance (Apr 25, 2022)
1-54139643-C-A		not specified	Uncertain significance (Apr 15, 2024)
1-54139645-T-TGC			Likely benign (Dec 01, 2022)
1-54139647-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-54139648-G-A		not specified	Uncertain significance (Jun 10, 2024)
1-54139743-C-T		not specified	Uncertain significance (May 29, 2024)
1-54139756-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-54139759-T-C		not specified	Uncertain significance (May 02, 2024)
1-54139776-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-54139785-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-54139794-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-54139891-C-T		not specified	Uncertain significance (Jan 31, 2022)
1-54139899-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-54139980-A-C		not specified	Uncertain significance (May 01, 2023)
1-54141124-C-G		not specified	Uncertain significance (Jun 06, 2023)
1-54141167-C-T		not specified	Uncertain significance (Mar 21, 2022)
1-54141182-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-54141194-G-C		not specified	Uncertain significance (Jun 24, 2022)
1-54141250-G-A		not specified	Uncertain significance (Jan 27, 2022)
1-54141289-T-A		not specified	Uncertain significance (May 04, 2023)
1-54141304-A-T		not specified	Uncertain significance (Nov 06, 2023)
1-54141323-G-A		not specified	Uncertain significance (Dec 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDCP2	protein_coding	protein_coding	ENST00000371330	4	20697

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.47e-11	0.0235	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0201	270	271	0.997	0.0000154	2904
Missense in Polyphen		100	105.11	0.95141		1161
Synonymous	0.104	122	123	0.988	0.00000785	956
Loss of Function	-0.653	14	11.6	1.21	4.94e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00185	0.00184
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.947
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.98

Haploinsufficiency Scores

• pHI: 0.0647
• hipred: N
• hipred_score: 0.197
• ghis: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.238

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdcp2

Gene ontology

• Cellular component: extracellular region