BCAM

basal cell adhesion molecule (Lutheran blood group), the group of CD molecules|C2-set domain containing|Ig-like cell adhesion molecule family|Blood group antigens

Basic information

Region (hg38): 19:44809071-44821421

Previous symbols: [ "LU" ]

Links

ENSG00000187244 ∙ NCBI:4059 ∙ OMIM:612773 ∙ HGNC:6722 ∙ Uniprot:P50895 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, Lutheran system; Blood group, Auberger system; Blood group, Lutheran null	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	14025138; 4836779; 1146276; 9192786; 9166867; 17319831; 18487511

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAM 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	4	7
missense			38	9	3	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding				2		2
Total	0	0	38	14	7

Variants in BCAM

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

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

Position	Type	Phenotype	Significance	ClinVar
19-44809173-C-G		not specified	Uncertain significance (Jun 07, 2023)
19-44811234-C-G		not specified	Uncertain significance (Jan 16, 2024)
19-44811258-C-T		BCAM-related disorder	Likely benign (Sep 10, 2019)
19-44812188-G-A		LUTHERAN BLOOD GROUP POLYMORPHISM Lu(a)/Lu(b)	Benign (-)
19-44812245-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-44812283-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-44812319-C-T		BLOOD GROUP--LUTHERAN NULL	Pathogenic (Aug 28, 2018)
19-44812328-G-A		not specified	Uncertain significance (Nov 29, 2023)
19-44812384-C-T			Likely benign (Sep 01, 2022)
19-44812385-G-A		not specified	Uncertain significance (Aug 14, 2023)
19-44812399-T-A		BCAM-related disorder	Likely benign (Jan 17, 2020)
19-44812483-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-44813302-A-G		not specified	Uncertain significance (Sep 14, 2022)
19-44813447-T-A		BCAM-related disorder	Likely benign (Oct 21, 2019)
19-44813455-C-G		not specified	Uncertain significance (Aug 08, 2023)
19-44813458-A-G		not specified	Uncertain significance (Jun 29, 2023)
19-44813460-G-C		BCAM-related disorder	Likely benign (Mar 12, 2019)
19-44813502-C-G			Likely benign (Jul 01, 2022)
19-44813527-C-T		BLOOD GROUP--LUTHERAN NULL	Pathogenic (Mar 01, 2007)
19-44813528-G-C		not specified	Uncertain significance (Apr 19, 2024)
19-44813547-C-A		BLOOD GROUP--LUTHERAN NULL	Pathogenic (Mar 01, 2007)
19-44813547-C-T		BCAM-related disorder	Benign (Dec 23, 2019)
19-44813550-C-T		BCAM-related disorder	Benign (Jan 02, 2020)
19-44813568-C-G			Benign (Jun 27, 2018)
19-44813570-A-T		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAM	protein_coding	protein_coding	ENST00000270233	15	12346

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-8	0.984	125690	1	53	125744	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	402	417	0.965	0.0000295	3966
Missense in Polyphen		138	148.81	0.92737		1383
Synonymous	-0.454	191	183	1.04	0.0000140	1346
Loss of Function	2.29	18	32.0	0.563	0.00000180	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000326
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000231	0.000217
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.000278	0.000264
Middle Eastern	0.000231	0.000217
South Asian	0.000264	0.000261
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Laminin alpha-5 receptor. May mediate intracellular signaling. {ECO:0000269|PubMed:9616226}.

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.674
• rvis_EVS: 1.25
• rvis_percentile_EVS: 93.48

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.313
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.717

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcam
• Phenotype: renal/urinary system phenotype; digestive/alimentary phenotype; normal 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); growth/size/body region phenotype

Gene ontology

• Biological process: cell adhesion;cell-matrix adhesion;signal transduction
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane;external side of plasma membrane;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: transmembrane signaling receptor activity;laminin receptor activity;protein binding;protein C-terminus binding;laminin binding