CD48

CD48 molecule, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 1:160678746-160711831

Previous symbols: [ "BCM1" ]

Links

ENSG00000117091 ∙ NCBI:962 ∙ OMIM:109530 ∙ HGNC:1683 ∙ Uniprot:P09326 ∙ 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 CD48 gene.

• not_specified (30 variants)
• not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD48 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001778.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	3	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD48	protein_coding	protein_coding	ENST00000368046	4	33106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000173	0.456	125719	0	2	125721	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0365	125	126	0.991	0.00000629	1589
Missense in Polyphen		28	31.115	0.89989		438
Synonymous	-0.138	53	51.7	1.02	0.00000285	464
Loss of Function	0.481	8	9.61	0.833	4.11e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand for CD2. Might facilitate interaction between activated lymphocytes. Probably involved in regulating T-cell activation.
• Pathway: Natural killer cell mediated cytotoxicity - Homo sapiens (human);Gastric Cancer Network 2;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.373

Intolerance Scores

• loftool: 0.661
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• pHI: 0.0695
• hipred: N
• hipred_score: 0.182
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.750

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd48
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: regulation of adaptive immune response;defense response;leukocyte migration
• Cellular component: plasma membrane;membrane;anchored component of membrane;intrinsic component of plasma membrane;membrane raft;extracellular exosome
• Molecular function: antigen binding;protein binding;signaling receptor activity