MADCAM1

mucosal vascular addressin cell adhesion molecule 1, the group of Immunoglobulin like domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 19:489175-505343

Links

ENSG00000099866 ∙ NCBI:8174 ∙ OMIM:102670 ∙ HGNC:6765 ∙ Uniprot:Q13477 ∙ 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 MADCAM1 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MADCAM1 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						0
missense			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in MADCAM1

This is a list of pathogenic ClinVar variants found in the MADCAM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-496528-C-T		not specified	Uncertain significance (Jun 30, 2023)
19-497907-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-497929-C-T		not specified	Uncertain significance (Aug 12, 2022)
19-497932-G-T		not specified	Uncertain significance (Jan 10, 2022)
19-497978-C-A		not specified	Uncertain significance (Jan 08, 2024)
19-497985-G-T		not specified	Uncertain significance (Nov 01, 2022)
19-498066-G-A		not specified	Uncertain significance (Feb 17, 2023)
19-498562-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-498639-G-T		not specified	Uncertain significance (Sep 22, 2023)
19-498663-C-G		not specified	Likely benign (Sep 14, 2023)
19-498669-G-A		not specified	Uncertain significance (Mar 12, 2024)
19-498717-G-A		not specified	Uncertain significance (Nov 12, 2021)
19-498747-C-T		not specified	Uncertain significance (May 24, 2023)
19-498781-T-G		not specified	Uncertain significance (Oct 29, 2021)
19-498811-G-A		not specified	Uncertain significance (Oct 16, 2023)
19-501690-C-T		not specified	Uncertain significance (Sep 26, 2023)
19-501698-C-T		not specified	Uncertain significance (Jan 22, 2024)
19-501701-G-GACACCACCTCCCCGGAGCCTCCCA		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
19-501720-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-501743-T-TCTCCCGACACCACCTCCCAGGAGCCTCCCGACACCACCTCCCAGGAGC		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
19-501875-C-G		not specified	Uncertain significance (Dec 20, 2023)
19-501903-C-T		not specified	Uncertain significance (May 25, 2022)
19-504774-G-A		not specified	Likely benign (Nov 17, 2022)
19-504813-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-504853-G-A		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MADCAM1	protein_coding	protein_coding	ENST00000215637	5	16172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.535	0.452	121666	309	1674	123649	0.00805

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.476	151	168	0.897	0.00000975	2320
Missense in Polyphen		19	27.868	0.68179		467
Synonymous	-0.370	90	85.6	1.05	0.00000580	881
Loss of Function	1.98	1	6.41	0.156	2.77e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.128	0.109
Ashkenazi Jewish	0.00213	0.000905
East Asian	0.00282	0.00240
Finnish	0.000819	0.000377
European (Non-Finnish)	0.00101	0.000757
Middle Eastern	0.00282	0.00240
South Asian	0.00234	0.00183
Other	0.00437	0.00382

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion leukocyte receptor expressed by mucosal venules, helps to direct lymphocyte traffic into mucosal tissues including the Peyer patches and the intestinal lamina propria. It can bind both integrin alpha-4/beta-7 and L-selectin, regulating both the passage and retention of leukocytes. Isoform 2, lacking the mucin-like domain, may be specialized in supporting integrin alpha-4/beta-7-dependent adhesion strengthening, independent of L- selectin binding.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Integrin cell surface interactions;Extracellular matrix organization;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;a4b7 Integrin signaling;Beta5 beta6 beta7 and beta8 integrin cell surface interactions (Consensus)

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.295

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.293

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Madcam1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: positive regulation of leukocyte migration;immune response;cell adhesion;cell-matrix adhesion;signal transduction;integrin-mediated signaling pathway;extracellular matrix organization;heterotypic cell-cell adhesion;receptor clustering;regulation of immune response;leukocyte tethering or rolling;positive regulation of lymphocyte migration
• Cellular component: plasma membrane;membrane;integral component of membrane
• Molecular function: integrin binding involved in cell-matrix adhesion