MARCHF1

membrane associated ring-CH-type finger 1, the group of Ring finger proteins|Membrane associated ring-CH-type fingers

Basic information

Region (hg38): 4:163524298-164384050

Previous symbols: [ "MARCH1" ]

Links

ENSG00000145416 ∙ NCBI:55016 ∙ OMIM:613331 ∙ HGNC:26077 ∙ Uniprot:Q8TCQ1 ∙ 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 MARCHF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MARCHF1 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in MARCHF1

This is a list of pathogenic ClinVar variants found in the MARCHF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-163528771-G-A		not specified	Uncertain significance (Feb 27, 2024)
4-163528832-A-C		not specified	Uncertain significance (Oct 04, 2022)
4-163528908-A-C		not specified	Uncertain significance (Jul 08, 2022)
4-163529041-G-A		not specified	Uncertain significance (May 30, 2024)
4-163585754-G-A		not specified	Uncertain significance (Jun 06, 2023)
4-163585773-C-G		not specified	Uncertain significance (Oct 20, 2023)
4-163585848-C-G		not specified	Uncertain significance (Oct 26, 2021)
4-163585902-C-G		not specified	Uncertain significance (Oct 12, 2022)
4-163613359-C-T		not specified	Uncertain significance (Nov 21, 2023)
4-163613365-G-A		not specified	Uncertain significance (Dec 13, 2022)
4-163854042-G-T		not specified	Uncertain significance (Dec 17, 2023)
4-163854046-G-T		not specified	Uncertain significance (Dec 15, 2022)
4-163854052-T-C		not specified	Uncertain significance (Jan 18, 2023)
4-163854056-C-T		not specified	Uncertain significance (Oct 14, 2021)
4-163854081-G-T		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MARCHF1	protein_coding	protein_coding	ENST00000503008	6	859753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00868	0.980	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	115	166	0.692	0.00000943	1870
Missense in Polyphen		37	78.764	0.46976		876
Synonymous	-0.198	62	60.0	1.03	0.00000332	569
Loss of Function	2.21	6	15.4	0.390	8.81e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000906
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000713	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination of TFRC, CD86, FAS and MHC class II proteins, such as HLA-DR alpha and beta, and promotes their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. By constitutively ubiquitinating MHC class II proteins in immature dendritic cells, down-regulates their cell surface localization thus sequestering them in the intracellular endosomal system. {ECO:0000269|PubMed:14722266, ECO:0000269|PubMed:18305173, ECO:0000269|PubMed:18389477, ECO:0000269|PubMed:19117940}.

Recessive Scores

• pRec: 0.0817

Intolerance Scores

• loftool: 0.599
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.498
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.552

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: March1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: protein polyubiquitination;antigen processing and presentation of peptide antigen via MHC class II;immune response
• Cellular component: lysosome;lysosomal membrane;endosome;endoplasmic reticulum membrane;plasma membrane;integral component of membrane;cytoplasmic vesicle membrane;early endosome membrane;late endosome membrane;trans-Golgi network membrane
• Molecular function: ubiquitin-protein transferase activity;zinc ion binding;MHC protein binding;ubiquitin protein ligase activity