CD302

protein-coding

CD302 molecule, the group of CD molecules|C-type lectin domain containing

Gene summary

CD302 is a C-type lectin receptor involved in cell adhesion and migration, as well as endocytosis and phagocytosis (Kato et al., 2007 [PubMed 17947679]).[supplied by OMIM, Aug 2008]

MANE transcript

NM_014880.5

Inheritance

—

ClinVar variants

U:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr2:159,768,628-159,798,255

External References & Databases

Ensembl (ENSG00000241399)

Transcript & Mutation Effects

hg38 • Region Span ~29.6 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 CD302 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014880.5. 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						0
missense			7 clinvar			7
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	8	0	0	8

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014880.5	RefSeq	NP_055695.2	6	MANE Select
ENST00000259053.6	Ensembl	ENSP00000259053.4	6	MANE Select
NM_001198763.2	RefSeq	NP_001185692.1	5	Standard
NM_001198764.2	RefSeq	NP_001185693.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

phagocytosis

Molecular Function

carbohydrate binding

Cellular Component

microvillus
cell cortex
membrane
integral component of membrane
filopodium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259053
Coding exons: 6
Length: 29390
Individuals with no LoFs: 125637
Homozygous LoFs: 1
Heterozygous LoFs: 101
Defined: 125739
p: 0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.109	117	114	1.03	0.00000536	1529
Missense (PolyPhen)		31	34.083	0.90955		471
Synonymous	0.782	34	40.3	0.843	0.00000200	418
Loss of Function	0.411	9	10.4	0.863	4.39e-7	144

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0044	0.0044	notable
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00016	0.00016	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Potential multifunctional C-type lectin receptor that may play roles in endocytosis and phagocytosis as well as in cell adhesion and migration. {ECO:0000269|PubMed:17947679}.;

Recessive Scores

pRec: 0.371

Intolerance Scores

LoFtool: 0.763
RVIS EVS: 0.33
RVIS percentile EVS: 73.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.246

Gene Damage Prediction

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