MUC6

protein-coding

mucin 6, oligomeric mucus/gel-forming, the group of Mucins

Gene summary

This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins produced by many epithelial tissues. The protein encoded by this gene is secreted and forms an insoluble mucous barrier that protects the gut lumen. [provided by RefSeq, Dec 2016]

MANE transcript

NM_005961.3

Inheritance

—

ClinVar variants

U:18B:22

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr11:1,012,823-1,036,718

External References & Databases

Ensembl (ENSG00000184956)

Transcript & Mutation Effects

hg38 • Region Span ~23.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MUC6 variants in ClinVar

5 Conditions Cataloged

not providedTotal: 23

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Prostate cancerTotal: 1

MUC6-related disorderTotal: 1

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005961.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	22 clinvar		24
missense			12 clinvar			12
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	18	22	0	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005961.3	RefSeq	NP_005952.2	33	MANE Select
ENST00000421673.7	Ensembl	ENSP00000406861.2	33	MANE Select
ENST00000525923.1	Ensembl	ENSP00000433790.1	3	Standard
ENST00000527242.2	Ensembl	ENSP00000436903.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gastric acid production
Post-translational protein modification
Dectin-2 family
Metabolism of proteins
C-type lectin receptors (CLRs)

Biological Process

stimulatory C-type lectin receptor signaling pathway
O-glycan processing
maintenance of gastrointestinal epithelium

Molecular Function

extracellular matrix structural constituent

Cellular Component

extracellular region
Golgi lumen
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000421673
Coding exons: 33
Length: 23886
Individuals with no LoFs: 124809
Homozygous LoFs: 3
Heterozygous LoFs: 565
Defined: 125377
p: 0.00227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.914	1263	1.36e+3	0.930	0.0000878	14736
Missense (PolyPhen)		49	73.028	0.67097		925
Synonymous	-0.328	631	621	1.02	0.0000475	5054
Loss of Function	1.77	70	87.9	0.796	0.00000454	942

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00065	0.00062	rare
Latino/Admixed American	0.0025	0.0024	notable
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.0014	0.0014	notable
Finnish	0.0015	0.0015	notable
European (Non-Finnish)	0.0033	0.0032	notable
South Asian	0.0015	0.0013	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May provide a mechanism for modulation of the composition of the protective mucus layer related to acid secretion or the presence of bacteria and noxious agents in the lumen. Plays an important role in the cytoprotection of epithelial surfaces and are used as tumor markers in a variety of cancers. May play a role in epithelial organogenesis. {ECO:0000269|PubMed:10209489, ECO:0000269|PubMed:10330458, ECO:0000269|PubMed:11988092}.;

Recessive Scores

pRec: 0.177

Intolerance Scores

LoFtool: 0.987
RVIS EVS: 1.26
RVIS percentile EVS: 93.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.126

Gene Damage Prediction

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