MARCHF2

membrane associated ring-CH-type finger 2, the group of Ring finger proteins|Membrane associated ring-CH-type fingers

Basic information

Region (hg38): 19:8413270-8439017

Previous symbols: [ "MARCH2" ]

Links

ENSG00000099785 ∙ NCBI:51257 ∙ OMIM:613332 ∙ HGNC:28038 ∙ Uniprot:Q9P0N8 ∙ 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 MARCHF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MARCHF2 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				2		2
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in MARCHF2

This is a list of pathogenic ClinVar variants found in the MARCHF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-8421845-C-T		not specified	Uncertain significance (May 09, 2024)
19-8421856-T-C		not specified	Uncertain significance (Mar 31, 2023)
19-8421892-G-A		not specified	Uncertain significance (Apr 18, 2023)
19-8421901-G-A		not specified	Uncertain significance (Sep 13, 2023)
19-8426634-C-T		not specified	Uncertain significance (May 06, 2022)
19-8426644-C-T		not specified	Uncertain significance (Feb 06, 2024)
19-8426649-G-A		not specified	Uncertain significance (Jun 02, 2023)
19-8426764-C-T		not specified	Uncertain significance (Oct 27, 2022)
19-8426770-T-C		not specified	Uncertain significance (May 31, 2023)
19-8430658-T-C		not specified	Uncertain significance (Jan 10, 2022)
19-8430677-C-T		not specified	Uncertain significance (Jun 02, 2024)
19-8430679-C-G		not specified	Uncertain significance (Feb 02, 2024)
19-8430767-G-A		not specified	Uncertain significance (Dec 27, 2022)
19-8430770-G-A		not specified	Uncertain significance (Jun 28, 2023)
19-8430824-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-8430851-A-G		not specified	Uncertain significance (Sep 14, 2022)
19-8430863-C-T		not specified	Uncertain significance (May 23, 2023)
19-8438430-A-G		not specified	Uncertain significance (Apr 12, 2023)
19-8438434-C-T		not specified	Uncertain significance (Jun 29, 2022)
19-8438459-C-T			Likely benign (Nov 01, 2022)
19-8438461-G-A		not specified	Uncertain significance (Feb 12, 2024)
19-8438476-C-T		not specified	Uncertain significance (Mar 12, 2024)
19-8438477-C-T			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MARCHF2	protein_coding	protein_coding	ENST00000602117	4	25748

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0330	0.931	125724	0	9	125733	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.922	135	169	0.800	0.0000117	1557
Missense in Polyphen		36	54.203	0.66417		482
Synonymous	0.00744	82	82.1	0.999	0.00000602	539
Loss of Function	1.81	4	10.3	0.390	5.02e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000106	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000528
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that may mediate ubiquitination of TFRC and CD86, 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. May be involved in endosomal trafficking through interaction with STX6. {ECO:0000269|PubMed:14722266, ECO:0000269|PubMed:15689499, ECO:0000269|PubMed:16428329}.

Intolerance Scores

• loftool: 0.454
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.252
• hipred: Y
• hipred_score: 0.503
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: March2

Zebrafish Information Network

• Gene name: march2
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: endocytosis;protein ubiquitination
• Cellular component: lysosomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;endosome membrane;integral component of membrane;cytoplasmic vesicle
• Molecular function: ubiquitin-protein transferase activity;protein binding;zinc ion binding