CDCP1

CUB domain containing protein 1, the group of CD molecules

Basic information

Region (hg38): 3:45082277-45146422

Links

ENSG00000163814 ∙ NCBI:64866 ∙ OMIM:611735 ∙ HGNC:24357 ∙ Uniprot:Q9H5V8 ∙ 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 CDCP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDCP1 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					1	1
missense			42	4	2	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	4	3

Variants in CDCP1

This is a list of pathogenic ClinVar variants found in the CDCP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-45085658-G-C		not specified	Uncertain significance (Dec 14, 2023)
3-45085699-C-T		not specified	Likely benign (Jan 30, 2024)
3-45085802-C-A		not specified	Uncertain significance (Dec 13, 2022)
3-45085805-T-C		not specified	Uncertain significance (Oct 17, 2023)
3-45085861-C-T			Benign (May 21, 2018)
3-45085895-C-T		not specified	Uncertain significance (Dec 13, 2022)
3-45085972-C-T		not specified	Uncertain significance (Dec 19, 2022)
3-45085975-C-T		not specified	Uncertain significance (Jul 25, 2023)
3-45085978-T-C		not specified	Uncertain significance (Mar 15, 2024)
3-45085979-T-A		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
3-45085989-T-G		not specified	Uncertain significance (Jun 13, 2024)
3-45086035-C-T		not specified	Uncertain significance (Mar 01, 2023)
3-45089123-A-G		not specified	Uncertain significance (Jun 29, 2022)
3-45089127-G-C		not specified	Uncertain significance (Apr 15, 2024)
3-45089130-T-C		not specified	Likely benign (Dec 14, 2023)
3-45091263-T-C		not specified	Uncertain significance (Oct 03, 2022)
3-45091299-C-T		not specified	Uncertain significance (Aug 16, 2021)
3-45091314-T-G		not specified	Uncertain significance (Apr 23, 2024)
3-45091332-G-A		not specified	Uncertain significance (Mar 18, 2024)
3-45091377-C-T		not specified	Uncertain significance (Mar 31, 2023)
3-45091380-C-T			Benign (May 24, 2018)
3-45091385-C-T		not specified	Uncertain significance (Sep 15, 2021)
3-45091414-C-G		not specified	Uncertain significance (Mar 28, 2022)
3-45091419-C-T		not specified	Likely benign (Apr 12, 2022)
3-45093281-G-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDCP1	protein_coding	protein_coding	ENST00000296129	9	64145

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000100	0.999	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	395	480	0.824	0.0000286	5482
Missense in Polyphen		97	159.95	0.60644		1918
Synonymous	0.842	187	202	0.925	0.0000129	1710
Loss of Function	3.03	12	29.8	0.402	0.00000165	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000272
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000932	0.0000879
Middle Eastern	0.000326	0.000272
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cell adhesion and cell matrix association. May play a role in the regulation of anchorage versus migration or proliferation versus differentiation via its phosphorylation. May be a novel marker for leukemia diagnosis and for immature hematopoietic stem cell subsets. Belongs to the tetraspanin web involved in tumor progression and metastasis. {ECO:0000269|PubMed:11466621, ECO:0000269|PubMed:12799299, ECO:0000269|PubMed:15153610, ECO:0000269|PubMed:16007225, ECO:0000269|PubMed:16404722, ECO:0000269|PubMed:8647901}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.362

Intolerance Scores

• loftool: 0.777
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.73

Haploinsufficiency Scores

• pHI: 0.113
• hipred: Y
• hipred_score: 0.598
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.158

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdcp1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; neoplasm

Gene ontology

• Cellular component: extracellular region;plasma membrane;integral component of membrane
• Molecular function: protein binding