CD300C

CD300c molecule, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 17:74534362-74546133

Links

ENSG00000167850 ∙ NCBI:10871 ∙ OMIM:606786 ∙ HGNC:19320 ∙ Uniprot:Q08708 ∙ 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 CD300C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD300C 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			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in CD300C

This is a list of pathogenic ClinVar variants found in the CD300C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74541674-C-G		not specified	Uncertain significance (Sep 01, 2021)
17-74541716-C-T		not specified	Likely benign (Jan 29, 2024)
17-74542880-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-74542897-G-A		not specified	Uncertain significance (Jun 07, 2023)
17-74542919-C-T		not specified	Uncertain significance (Feb 10, 2022)
17-74542930-G-A		not specified	Uncertain significance (Aug 08, 2023)
17-74542981-G-A		not specified	Uncertain significance (Apr 15, 2024)
17-74542984-C-T		not specified	Uncertain significance (Oct 05, 2023)
17-74544624-C-A		not specified	Uncertain significance (Jun 13, 2024)
17-74544633-C-T		not specified	Uncertain significance (Sep 16, 2021)
17-74544656-C-T		not specified	Likely benign (Sep 06, 2022)
17-74544665-G-A		not specified	Uncertain significance (Aug 17, 2021)
17-74544732-A-G		not specified	Uncertain significance (Jun 17, 2022)
17-74544806-A-G		not specified	Uncertain significance (Mar 29, 2022)
17-74544833-G-T		not specified	Uncertain significance (Nov 01, 2022)
17-74544891-T-C		not specified	Uncertain significance (May 26, 2022)
17-74544938-G-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD300C	protein_coding	protein_coding	ENST00000330793	4	5036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000116	0.381	125724	0	13	125737	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.429	121	135	0.896	0.00000767	1432
Missense in Polyphen		34	35.433	0.95956		438
Synonymous	0.359	53	56.4	0.939	0.00000339	468
Loss of Function	0.318	8	9.03	0.886	5.57e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.687
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0611
• hipred: N
• hipred_score: 0.112
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.194

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd300c2
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: immune system process;cellular defense response;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: transmembrane signaling receptor activity