MARVELD3

MARVEL domain containing 3, the group of MARVEL domain containing

Basic information

Region (hg38): 16:71626161-71642114

Previous symbols: [ "MRVLDC3" ]

Links

ENSG00000140832 ∙ NCBI:91862 ∙ OMIM:614094 ∙ HGNC:30525 ∙ Uniprot:Q96A59 ∙ 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 MARVELD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MARVELD3 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	17	1	0

Variants in MARVELD3

This is a list of pathogenic ClinVar variants found in the MARVELD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-71626245-G-C		not specified	Uncertain significance (Apr 08, 2024)
16-71626261-G-A		not specified	Uncertain significance (Apr 25, 2022)
16-71626261-G-C		not specified	Uncertain significance (Dec 13, 2021)
16-71626291-G-T		not specified	Uncertain significance (Jan 24, 2023)
16-71626297-C-T		not specified	Uncertain significance (Aug 16, 2021)
16-71626311-G-A		not specified	Uncertain significance (Dec 08, 2021)
16-71626323-G-T		not specified	Uncertain significance (Sep 06, 2022)
16-71626339-G-A		not specified	Uncertain significance (Feb 12, 2024)
16-71626350-C-A		not specified	Likely benign (Oct 04, 2022)
16-71626374-G-T		not specified	Uncertain significance (Mar 29, 2023)
16-71626412-A-C		not specified	Uncertain significance (Feb 06, 2024)
16-71626498-G-T		not specified	Uncertain significance (Nov 08, 2022)
16-71626539-C-T		not specified	Uncertain significance (Nov 22, 2022)
16-71626551-G-A		not specified	Uncertain significance (Feb 10, 2022)
16-71626557-C-A		not specified	Uncertain significance (Jun 13, 2022)
16-71626587-C-T		not specified	Uncertain significance (Sep 15, 2021)
16-71626664-G-T		not specified	Uncertain significance (Jun 13, 2024)
16-71626677-G-A		not specified	Uncertain significance (Jun 03, 2022)
16-71629375-C-T		not specified	Uncertain significance (Jun 10, 2024)
16-71640475-T-A		not specified	Uncertain significance (Oct 29, 2021)
16-71640944-G-A		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MARVELD3	protein_coding	protein_coding	ENST00000299952	3	15954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.59e-7	0.507	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.365	243	260	0.936	0.0000150	2582
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000366	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000152	0.000141
Middle Eastern	0.000366	0.000326
South Asian	0.000276	0.000261
Other	0.000403	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a component of tight junctions, plays a role in paracellular ion conductivity. {ECO:0000269|PubMed:20028514}.
• Pathway: Tight junction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0818

Intolerance Scores

• loftool: 0.376
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.355
• hipred: N
• hipred_score: 0.180
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.332

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Marveld3

Gene ontology

• 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;bicellular tight junction assembly;protein localization to cell junction
• Cellular component: bicellular tight junction;integral component of membrane;cytoplasmic vesicle
• Molecular function: protein binding;mitogen-activated protein kinase kinase kinase binding