MARCHF3

membrane associated ring-CH-type finger 3, the group of Ring finger proteins|Membrane associated ring-CH-type fingers

Basic information

Region (hg38): 5:126867714-127030558

Previous symbols: [ "MARCH3" ]

Links

ENSG00000173926 ∙ NCBI:115123 ∙ OMIM:613333 ∙ HGNC:28728 ∙ Uniprot:Q86UD3 ∙ 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 MARCHF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MARCHF3 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in MARCHF3

This is a list of pathogenic ClinVar variants found in the MARCHF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-126870670-T-C		not specified	Uncertain significance (Nov 30, 2022)
5-126870725-G-A		not specified	Uncertain significance (Feb 22, 2023)
5-126870748-C-T		not specified	Uncertain significance (Sep 07, 2022)
5-126870749-G-A		not specified	Uncertain significance (Apr 28, 2022)
5-126870751-C-T		not specified	Uncertain significance (Feb 16, 2023)
5-126870760-T-C		not specified	Uncertain significance (Oct 06, 2022)
5-126870763-T-A		not specified	Uncertain significance (Dec 28, 2022)
5-126870767-A-C		not specified	Uncertain significance (Jan 23, 2023)
5-126870769-C-T		not specified	Uncertain significance (Oct 04, 2024)
5-126878217-C-T		not specified	Uncertain significance (Nov 15, 2021)
5-126878252-C-T		not specified	Uncertain significance (Dec 17, 2023)
5-126878280-C-T		not specified	Uncertain significance (Aug 05, 2023)
5-126878360-C-T		not specified	Uncertain significance (Feb 22, 2023)
5-126914953-G-A		not specified	Uncertain significance (Feb 06, 2024)
5-126915048-G-T		not specified	Uncertain significance (May 28, 2024)
5-126915126-T-C		not specified	Uncertain significance (Apr 13, 2022)
5-126918087-C-A		not specified	Uncertain significance (Mar 29, 2023)
5-126918095-G-A		not specified	Uncertain significance (Feb 06, 2023)
5-126918096-T-C		not specified	Uncertain significance (Jun 03, 2024)
5-126918105-C-T		not specified	Uncertain significance (Dec 26, 2023)
5-126918141-C-T		not specified	Uncertain significance (Jan 08, 2025)
5-126918150-G-T		not specified	Uncertain significance (Sep 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MARCHF3	protein_coding	protein_coding	ENST00000308660	4	163095

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.173	0.815	125735	0	11	125746	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.885	127	158	0.802	0.00000981	1627
Missense in Polyphen		28	44.117	0.63467		472
Synonymous	-1.90	86	66.4	1.30	0.00000403	531
Loss of Function	2.17	3	10.6	0.282	5.20e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which may be involved in endosomal trafficking. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. {ECO:0000250|UniProtKB:Q5XIE5}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.337
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.734
• hipred: N
• hipred_score: 0.413
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.790

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: March3

Gene ontology

• Biological process: endocytosis;protein ubiquitination
• Cellular component: lysosome;endosome;integral component of membrane;cytoplasmic vesicle membrane;early endosome membrane;intracellular membrane-bounded organelle
• Molecular function: zinc ion binding;transferase activity