MARVELD3

protein-coding

MARVEL domain containing 3, the group of MARVEL domain containing

Gene summary

Enables mitogen-activated protein kinase kinase kinase binding activity. Involved in bicellular tight junction assembly. Acts upstream of or within several processes, including negative regulation of JNK cascade; negative regulation of epithelial cell migration; and negative regulation of epithelial cell proliferation. Located in bicellular tight junction and cytoplasmic vesicle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

MRVLDC3

MANE transcript

NM_052858.6

Inheritance

—

ClinVar variants

U:45B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr16:71,626,161-71,642,114

External References & Databases

Ensembl (ENSG00000140832)

Transcript & Mutation Effects

hg38 • Region Span ~16.0 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 MARVELD3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052858.6. 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			1 clinvar			1
missense			43 clinvar	3 clinvar		46
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	3	0	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052858.6	RefSeq	NP_443090.4	3	MANE Select
ENST00000268485.8	Ensembl	ENSP00000268485.3	3	MANE Select
NM_001017967.4	RefSeq	NP_001017967.2	3	Standard
NM_001271329.2	RefSeq	NP_001258258.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Tight junction - Homo sapiens (human)

Biological Process

response to osmotic stress
negative regulation of epithelial cell migration
cell-cell junction organization
negative regulation of JNK cascade
negative regulation of epithelial cell proliferation

Molecular Function

protein binding
mitogen-activated protein kinase kinase kinase binding

Cellular Component

bicellular tight junction
integral component of membrane
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299952
Coding exons: 3
Length: 15954
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 125747
p: 0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.365	243	260	0.936	0.0000150	2582
Missense (PolyPhen)		83	88.965	0.93295		921
Synonymous	-0.484	119	112	1.06	0.00000714	897
Loss of Function	0.871	12	15.7	0.763	8.49e-7	159

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00037	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00014	rare
South Asian	0.00028	0.00026	rare
Other	0.00040	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: As a component of tight junctions, plays a role in paracellular ion conductivity. {ECO:0000269|PubMed:20028514}.;

Recessive Scores

pRec: 0.0818

Intolerance Scores

LoFtool: 0.376
RVIS EVS: 0.07
RVIS percentile EVS: 58.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.332

Gene Damage Prediction

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