MUC2

mucin 2, oligomeric mucus/gel-forming, the group of Mucins

Basic information

Region (hg38): 11:1074874-1110511

Links

ENSG00000198788 ∙ NCBI:4583 ∙ OMIM:158370 ∙ HGNC:7512 ∙ Uniprot:Q02817 ∙ 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 MUC2 gene.

• not provided (27 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MUC2 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				24	1	25
missense				2		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	26	1

Variants in MUC2

This is a list of pathogenic ClinVar variants found in the MUC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-1075913-C-T			Likely benign (May 01, 2022)
11-1078371-G-A			Likely benign (Mar 01, 2023)
11-1078374-G-T			Likely benign (Nov 01, 2023)
11-1078394-C-T			Likely benign (Dec 01, 2022)
11-1078494-C-T			Likely benign (Oct 01, 2022)
11-1078509-C-T			Likely benign (Jul 01, 2023)
11-1082921-C-G			Likely benign (Feb 01, 2024)
11-1083094-C-T			Benign (Nov 01, 2023)
11-1084642-C-T			Likely benign (Apr 01, 2022)
11-1085192-C-T			Likely benign (Mar 01, 2023)
11-1085594-C-T			Likely benign (Dec 01, 2022)
11-1086284-C-T			Likely benign (Mar 01, 2023)
11-1088404-C-T			Likely benign (Jan 01, 2023)
11-1089970-G-A			Likely benign (Dec 01, 2022)
11-1094275-C-T			Likely benign (Nov 01, 2023)
11-1094452-T-G			Likely benign (Apr 01, 2024)
11-1094455-C-T			Likely benign (Apr 01, 2024)
11-1094482-G-A			Likely benign (Mar 01, 2023)
11-1094578-G-T			Likely benign (Mar 01, 2023)
11-1094590-A-C			Likely benign (Aug 01, 2023)
11-1094596-C-T			Likely benign (Aug 01, 2023)
11-1094680-T-A			Likely benign (Apr 01, 2024)
11-1094815-C-T			Likely benign (Aug 01, 2023)
11-1094857-T-C			Likely benign (Apr 01, 2024)
11-1094860-C-A			Likely benign (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MUC2	protein_coding	protein_coding	ENST00000441003	49	29545

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.43e-10	1.00	123930	0	967	124897	0.00388

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	1602	1.76e+3	0.912	0.000114	17944
Missense in Polyphen		390	485.91	0.80262		5124
Synonymous	-3.79	912	778	1.17	0.0000616	5708
Loss of Function	6.90	40	122	0.327	0.00000588	1367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0106	0.0105
Ashkenazi Jewish	0.00896	0.00878
East Asian	0.00310	0.00295
Finnish	0.00270	0.00265
European (Non-Finnish)	0.00270	0.00250
Middle Eastern	0.00310	0.00295
South Asian	0.00476	0.00468
Other	0.00532	0.00511

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Coats the epithelia of the intestines, airways, and other mucus membrane-containing organs. Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces. Major constituent of both the inner and outer mucus layers of the colon and may play a role in excluding bacteria from the inner mucus layer. {ECO:0000269|PubMed:19432394}.
• Pathway: Gastric cancer - Homo sapiens (human);Amoebiasis - Homo sapiens (human);trefoil factors initiate mucosal healing;nfkb activation by nontypeable hemophilus influenzae;Post-translational protein modification;Dectin-2 family;Metabolism of proteins;C-type lectin receptors (CLRs);Innate Immune System;Immune System;Termination of O-glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.313

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Muc2
• Phenotype: digestive/alimentary phenotype; immune system 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); growth/size/body region phenotype; neoplasm; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: stimulatory C-type lectin receptor signaling pathway;O-glycan processing;maintenance of gastrointestinal epithelium
• Cellular component: Golgi lumen;plasma membrane;inner mucus layer;outer mucus layer
• Molecular function: protein binding