CD302

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

Basic information

Region (hg38): 2:159768628-159798255

Links

ENSG00000241399 ∙ NCBI:9936 ∙ OMIM:612246 ∙ HGNC:30843 ∙ Uniprot:Q8IX05 ∙ 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 CD302 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD302 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in CD302

This is a list of pathogenic ClinVar variants found in the CD302 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-159771955-A-G		not specified	Uncertain significance (Mar 19, 2024)
2-159798165-G-A		not specified	Uncertain significance (Aug 20, 2024)
2-159798179-G-C		not specified	Uncertain significance (Nov 07, 2022)
2-159798182-A-C		not specified	Uncertain significance (Oct 03, 2022)
2-159798186-C-T		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD302	protein_coding	protein_coding	ENST00000259053	6	29390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000374	0.377	125637	1	101	125739	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.109	117	114	1.03	0.00000536	1529
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00455	0.00449
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000218	0.000217
South Asian	0.000163	0.000163
Other	0.000326	0.000326

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.325
• hipred: N
• hipred_score: 0.146
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.246

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd302

Gene ontology

• Biological process: phagocytosis
• Cellular component: microvillus;cell cortex;membrane;integral component of membrane;filopodium
• Molecular function: carbohydrate binding