CDCP1

protein-coding

CUB domain containing protein 1, the group of CD molecules

Gene summary

This gene encodes a transmembrane protein which contains three extracellular CUB domains and acts as a substrate for Src family kinases. The protein plays a role in the tyrosine phosphorylation-dependent regulation of cellular events that are involved in tumor invasion and metastasis. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

MANE transcript

NM_022842.5

Inheritance

—

ClinVar variants

U:116B:9

Top phenotype

Myoepithelial tumor

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr3:45,082,277-45,146,422

External References & Databases

Ensembl (ENSG00000163814)

Transcript & Mutation Effects

hg38 • Region Span ~64.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDCP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 115

not providedTotal: 3

Myoepithelial tumorTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022842.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			111 clinvar	6 clinvar	2 clinvar	119
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	116	6	3	125

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022842.5	RefSeq	NP_073753.3	9	MANE Select
ENST00000296129.6	Ensembl	ENSP00000296129.1	9	MANE Select
NM_178181.3	RefSeq	NP_835488.1	4	Standard
ENST00000425231.2	Ensembl	ENSP00000399342.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Molecular Function

protein binding

Cellular Component

extracellular region
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296129
Coding exons: 9
Length: 64145
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125748
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.37	395	480	0.824	0.0000286	5482
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00027	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.000093	0.000088	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.362

Intolerance Scores

LoFtool: 0.777
RVIS EVS: 0.27
RVIS percentile EVS: 70.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.158

Gene Damage Prediction

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