MARCHF4

membrane associated ring-CH-type finger 4, the group of Ring finger proteins|Membrane associated ring-CH-type fingers

Basic information

Region (hg38): 2:216257865-216372483

Previous symbols: [ "MARCH4" ]

Links

ENSG00000144583 ∙ NCBI:57574 ∙ OMIM:608208 ∙ HGNC:29269 ∙ Uniprot:Q9P2E8 ∙ 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 MARCHF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MARCHF4 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					1	1
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	1

Variants in MARCHF4

This is a list of pathogenic ClinVar variants found in the MARCHF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-216259316-A-G		not specified	Uncertain significance (Aug 17, 2022)
2-216259317-C-G		not specified	Uncertain significance (Sep 07, 2022)
2-216259367-T-C		not specified	Uncertain significance (Dec 01, 2022)
2-216259491-C-T		not specified	Uncertain significance (Mar 07, 2023)
2-216259530-A-G		not specified	Uncertain significance (Apr 13, 2022)
2-216259563-C-T		not specified	Uncertain significance (May 16, 2024)
2-216259574-T-C		not specified	Uncertain significance (Jan 04, 2022)
2-216259646-C-T		not specified	Uncertain significance (Jul 26, 2022)
2-216259654-C-T			Benign (May 24, 2018)
2-216277675-T-G		not specified	Uncertain significance (Sep 29, 2022)
2-216277705-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-216277743-C-A		not specified	Uncertain significance (Jan 24, 2023)
2-216277789-C-T		not specified	Uncertain significance (May 09, 2023)
2-216283615-T-C		Frontotemporal dementia	Uncertain significance (-)
2-216369785-C-T		not specified	Uncertain significance (Jun 05, 2024)
2-216369798-C-T		not specified	Uncertain significance (Jul 19, 2022)
2-216369812-A-G		not specified	Uncertain significance (Apr 23, 2024)
2-216369822-G-T		not specified	Uncertain significance (Jan 24, 2023)
2-216369866-C-A		not specified	Uncertain significance (Feb 14, 2023)
2-216369927-G-A		not specified	Uncertain significance (Mar 28, 2024)
2-216369974-A-C		not specified	Likely benign (Dec 08, 2023)
2-216370004-C-A		not specified	Uncertain significance (May 10, 2022)
2-216370033-G-T		not specified	Uncertain significance (Oct 26, 2022)
2-216370130-A-C		not specified	Uncertain significance (Dec 21, 2023)
2-216370181-G-A		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MARCHF4	protein_coding	protein_coding	ENST00000273067	4	114163

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.133	0.866	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	196	247	0.795	0.0000144	2628
Missense in Polyphen		48	75.474	0.63598		800
Synonymous	-0.852	114	103	1.11	0.00000644	835
Loss of Function	2.92	5	18.6	0.269	8.39e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000136	0.000132
Middle Eastern	0.0000545	0.0000544
South Asian	0.000300	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that may mediate ubiquitination of MHC-I and CD4, and promote their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. 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:0000269|PubMed:14722266}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.317
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.198
• hipred: Y
• hipred_score: 0.525
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: March4

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: Golgi membrane;Golgi stack;trans-Golgi network;integral component of membrane
• Molecular function: ubiquitin-protein transferase activity;zinc ion binding