CD82

CD82 molecule, the group of Tetraspanins|CD molecules

Basic information

Region (hg38): 11:44564427-44620363

Previous symbols: [ "ST6", "KAI1" ]

Links

ENSG00000085117 ∙ NCBI:3732 ∙ OMIM:600623 ∙ HGNC:6210 ∙ Uniprot:P27701 ∙ 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 CD82 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD82 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					3	3
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	3

Variants in CD82

This is a list of pathogenic ClinVar variants found in the CD82 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-44600189-T-C		not specified	Uncertain significance (Jan 09, 2024)
11-44600218-A-G		not specified	Uncertain significance (Aug 17, 2021)
11-44605090-T-C		not specified	Uncertain significance (Jan 24, 2024)
11-44605107-G-A			Benign (Jun 14, 2018)
11-44605147-G-A		not specified	Uncertain significance (Dec 14, 2022)
11-44618217-T-G		not specified	Uncertain significance (Feb 28, 2024)
11-44618240-C-T		not specified	Uncertain significance (Oct 29, 2021)
11-44618302-C-T			Uncertain significance (-)
11-44618303-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-44618307-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-44618338-C-G		not specified	Uncertain significance (Jan 09, 2024)
11-44618648-G-A		not specified	Uncertain significance (May 25, 2022)
11-44618650-A-G		not specified	Uncertain significance (Nov 05, 2021)
11-44618677-A-C		not specified	Uncertain significance (Jan 19, 2024)
11-44618688-A-G		not specified	Uncertain significance (Oct 26, 2021)
11-44618696-C-T			Benign (Oct 19, 2017)
11-44618721-G-A		not specified	Uncertain significance (Aug 29, 2022)
11-44619066-G-C			Benign (Jun 14, 2018)
11-44619082-C-T			Uncertain significance (-)
11-44619115-C-T		not specified	Uncertain significance (Apr 13, 2022)
11-44619122-A-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD82	protein_coding	protein_coding	ENST00000227155	8	55937

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-8	0.356	125707	1	40	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0899	165	168	0.981	0.0000102	1755
Missense in Polyphen		64	68.622	0.93265		722
Synonymous	-0.0580	73	72.4	1.01	0.00000505	494
Loss of Function	0.763	14	17.4	0.803	9.94e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.00	0.00
South Asian	0.000392	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with CD4 or CD8 and delivers costimulatory signals for the TCR/CD3 pathway.
• Pathway: p53 signaling pathway - Homo sapiens (human);TCR;Direct p53 effectors;Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.420

Intolerance Scores

• loftool: 0.386
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.272
• hipred: Y
• hipred_score: 0.669
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd82
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;extracellular exosome
• Molecular function: protein binding