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.

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.

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				1	2	3
missense			21	2	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	3

Variants in CD48

This is a list of pathogenic ClinVar variants found in the CD48 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160679081-G-A		not specified	Uncertain significance (Dec 23, 2024)
1-160679085-C-T			Likely benign (Jan 01, 2023)
1-160679098-C-G		not specified	Uncertain significance (May 11, 2022)
1-160681129-C-A			Benign (Dec 31, 2019)
1-160681220-T-C		not specified	Uncertain significance (Apr 22, 2024)
1-160681247-T-C		not specified	Uncertain significance (Aug 15, 2023)
1-160681262-C-T		not specified	Uncertain significance (Dec 17, 2023)
1-160681279-C-A		not specified	Uncertain significance (Mar 22, 2023)
1-160681320-G-C		not specified	Uncertain significance (Oct 09, 2024)
1-160681388-T-C		not specified	Uncertain significance (May 04, 2022)
1-160681468-T-C		not specified	Uncertain significance (Mar 08, 2025)
1-160684895-T-C		not specified	Uncertain significance (Mar 01, 2023)
1-160684898-A-T		not specified	Uncertain significance (Nov 19, 2022)
1-160684929-T-A		not specified	Uncertain significance (Sep 15, 2021)
1-160684945-C-T		not specified	Uncertain significance (Jul 05, 2023)
1-160684982-G-A		not specified	Uncertain significance (Jan 21, 2025)
1-160684995-C-T		not specified	Uncertain significance (Sep 09, 2024)
1-160685002-C-T			Benign (Dec 31, 2019)
1-160685026-T-A		not specified	Uncertain significance (May 09, 2023)
1-160685036-G-T		not specified	Uncertain significance (Oct 05, 2023)
1-160685067-A-G			Likely benign (Aug 01, 2022)
1-160685091-T-C		not specified	Uncertain significance (Jun 28, 2023)
1-160685093-T-C		not specified	Uncertain significance (Jul 19, 2023)
1-160685141-T-A		not specified	Uncertain significance (Aug 10, 2021)
1-160685151-C-T		not specified	Uncertain significance (Jan 03, 2024)

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