MCAM

melanoma cell adhesion molecule, the group of MicroRNA protein coding host genes|V-set domain containing|CD molecules|C2-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 11:119308529-119321521

Links

ENSG00000076706 ∙ NCBI:4162 ∙ OMIM:155735 ∙ HGNC:6934 ∙ Uniprot:P43121 ∙ 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 MCAM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCAM 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	1
missense			41	3	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	3	2

Variants in MCAM

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

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

Position	Type	Phenotype	Significance	ClinVar
11-119310386-T-G		not specified	Uncertain significance (Sep 09, 2024)
11-119310412-C-A		not specified	Uncertain significance (Nov 25, 2024)
11-119310414-T-C		not specified	Uncertain significance (Jun 29, 2023)
11-119310449-C-T		not specified	Uncertain significance (Oct 26, 2021)
11-119310459-G-T		not specified	Uncertain significance (Mar 26, 2024)
11-119310464-G-A		not specified	Uncertain significance (Apr 13, 2022)
11-119310792-C-T		not specified	Uncertain significance (Dec 01, 2022)
11-119310816-A-G		not specified	Uncertain significance (Aug 28, 2024)
11-119310830-C-T			Benign (Jul 06, 2018)
11-119310831-G-A		not specified	Uncertain significance (Feb 15, 2023)
11-119310834-A-G		not specified	Uncertain significance (Nov 18, 2022)
11-119310852-A-G		not specified	Likely benign (Dec 13, 2023)
11-119310876-C-T		not specified	Likely benign (Aug 21, 2024)
11-119310885-G-A		not specified	Uncertain significance (Aug 30, 2021)
11-119310891-G-A		not specified	Uncertain significance (Oct 10, 2023)
11-119311098-G-T		not specified	Uncertain significance (Jun 21, 2021)
11-119311117-G-A		not specified	Uncertain significance (Oct 29, 2024)
11-119311286-C-T		not specified	Uncertain significance (Jan 23, 2023)
11-119311412-G-C		not specified	Uncertain significance (Mar 31, 2024)
11-119311414-T-A		not specified	Uncertain significance (Feb 28, 2023)
11-119311417-C-T		not specified	Uncertain significance (Dec 17, 2023)
11-119311576-G-A		not specified	Uncertain significance (May 20, 2024)
11-119311598-C-G		not specified	Uncertain significance (Dec 22, 2023)
11-119311633-A-T		not specified	Uncertain significance (Dec 16, 2023)
11-119311822-T-A		not specified	Uncertain significance (Jun 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCAM	protein_coding	protein_coding	ENST00000264036	16	12991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000160	1.00	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.866	344	392	0.877	0.0000247	4175
Missense in Polyphen		109	146.39	0.74458		1586
Synonymous	-0.479	174	166	1.05	0.0000113	1310
Loss of Function	3.50	13	35.5	0.366	0.00000179	395

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000435	0.000435
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000435	0.000435
South Asian	0.000425	0.000425
Other	0.000174	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in cell adhesion, and in cohesion of the endothelial monolayer at intercellular junctions in vascular tissue. Its expression may allow melanoma cells to interact with cellular elements of the vascular system, thereby enhancing hematogeneous tumor spread. Could be an adhesion molecule active in neural crest cells during embryonic development. Acts as surface receptor that triggers tyrosine phosphorylation of FYN and PTK2/FAK1, and a transient increase in the intracellular calcium concentration. {ECO:0000269|PubMed:11036077, ECO:0000269|PubMed:8292890}.

Recessive Scores

• pRec: 0.331

Intolerance Scores

• loftool: 0.753
• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.89

Haploinsufficiency Scores

• pHI: 0.282
• hipred: N
• hipred_score: 0.483
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mcam
• Phenotype: immune 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); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: mcamb
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: angiogenesis;glomerular filtration;cell adhesion;anatomical structure morphogenesis;positive regulation of cell migration;vascular wound healing
• Cellular component: extracellular region;extracellular space;nucleus;plasma membrane;focal adhesion;external side of plasma membrane;integral component of membrane