CD151

CD151 molecule (Raph blood group), the group of Tetraspanins|CD molecules|Blood group antigens

Basic information

Region (hg38): 11:832886-839831

Links

ENSG00000177697 ∙ NCBI:977 ∙ OMIM:602243 ∙ HGNC:1630 ∙ Uniprot:P48509 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epidermolysis bullosa simplex 7, with nephropathy and deafness (Strong), mode of inheritance: AR
• epidermolysis bullosa simplex 7, with nephropathy and deafness (Strong), mode of inheritance: AR
• epidermolysis bullosa simplex 7, with nephropathy and deafness (Moderate), mode of inheritance: AR
• epidermolysis bullosa simplex 7, with nephropathy and deafness (Supportive), mode of inheritance: AR
• epidermolysis bullosa simplex 7, with nephropathy and deafness (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Raph blood group	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Audiologic/Otolaryngologic; Dermatologic; Hematologic; Renal	3604155; 3238950; 3412548; 15265795; 18522704
Individuals with Nephropathy with pretibial epidermolysis bullosa and deafness may manifest with deafness, but it is described as typically postlingual

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD151 gene.

• not provided (119 variants)
• Epidermolysis bullosa simplex 7, with nephropathy and deafness;RAPH BLOOD GROUP SYSTEM (9 variants)
• Inborn genetic diseases (9 variants)
• Epidermolysis bullosa simplex 7, with nephropathy and deafness (5 variants)
• RAPH BLOOD GROUP SYSTEM;Epidermolysis bullosa simplex 7, with nephropathy and deafness (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD151 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			2	22	2	26
missense			37	4	1	42
nonsense	1		2			3
start loss						0
frameshift						0
inframe indel		1	1			2
splice donor/acceptor (+/-2bp)				1		1
splice region			1	5	1	7
non coding			1	25	19	45
Total	1	1	43	52	22

Highest pathogenic variant AF is 0.00000657

Variants in CD151

This is a list of pathogenic ClinVar variants found in the CD151 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-835772-T-C			Benign (Nov 11, 2018)
11-835877-C-T			Benign (Nov 10, 2018)
11-835878-G-A			Likely benign (Mar 07, 2020)
11-836008-T-C			Benign (Nov 10, 2018)
11-836023-C-T			Benign (Nov 10, 2018)
11-836043-C-T		Epidermolysis bullosa simplex 7, with nephropathy and deafness;RAPH BLOOD GROUP SYSTEM	Likely benign (Jan 03, 2022)
11-836084-C-T			Likely benign (Oct 28, 2022)
11-836085-G-A		RAPH BLOOD GROUP SYSTEM;Epidermolysis bullosa simplex 7, with nephropathy and deafness	Uncertain significance (Dec 31, 2023)
11-836088-A-T		Epidermolysis bullosa simplex 7, with nephropathy and deafness	Pathogenic (Jun 24, 2020)
11-836092-A-C		CD151-related disorder	Benign/Likely benign (Jan 31, 2024)
11-836092-AGAC-A			Uncertain significance (May 18, 2022)
11-836109-G-C			Uncertain significance (Dec 30, 2023)
11-836138-C-T		CD151-related disorder	Likely benign (Nov 04, 2023)
11-836166-C-T		not specified	Benign/Likely benign (Dec 25, 2023)
11-836167-G-A			Likely benign (Nov 10, 2023)
11-836169-C-A			Likely benign (Oct 04, 2023)
11-836170-T-TTGCCCC			Likely benign (Sep 06, 2022)
11-836172-GCCCCCA-G			Likely benign (Jan 09, 2024)
11-836172-GCCCCCACCCCCA-G			Likely benign (Oct 03, 2022)
11-836172-G-GCCCCCA			Benign/Likely benign (Jan 21, 2024)
11-836227-A-G			Benign (Nov 10, 2018)
11-836270-T-C			Uncertain significance (Jul 06, 2022)
11-836296-C-T			Uncertain significance (Nov 15, 2022)
11-836311-A-G		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
11-836315-G-C			Uncertain significance (Aug 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD151	protein_coding	protein_coding	ENST00000397420	7	6989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000108	0.819	125228	0	21	125249	0.0000838

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.594	135	156	0.866	0.00000927	1639
Missense in Polyphen		33	45.49	0.72543		523
Synonymous	-1.85	84	65.0	1.29	0.00000407	497
Loss of Function	1.32	10	15.6	0.641	8.34e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000124	0.000124
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for the proper assembly of the glomerular and tubular basement membranes in kidney. {ECO:0000269|PubMed:15265795}.
• Disease: DISEASE: Nephropathy with pretibial epidermolysis bullosa and deafness (NPEBD) [MIM:609057]: A disorder characterized by the association of hereditary nephritis, epidermolysis bullosa, deafness, and beta-thalassemia minor. {ECO:0000269|PubMed:15265795}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Primary Focal Segmental Glomerulosclerosis FSGS;Assembly of collagen fibrils and other multimeric structures;Alpha6Beta4Integrin;Collagen formation;Extracellular matrix organization;Type I hemidesmosome assembly;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.249

Intolerance Scores

• loftool: 0.272
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.162
• hipred: Y
• hipred_score: 0.685
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.802

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd151
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; 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); neoplasm; immune system phenotype; renal/urinary system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell adhesion;cell surface receptor signaling pathway;positive regulation of cell migration;hemidesmosome assembly;T cell proliferation;wound healing, spreading of cells;positive regulation of endocytosis
• Cellular component: basement membrane;cytosol;plasma membrane;integral component of plasma membrane;focal adhesion;cell surface;membrane
• Molecular function: integrin binding;protein binding