MARCHF9

membrane associated ring-CH-type finger 9, the group of Membrane associated ring-CH-type fingers|Ring finger proteins

Basic information

Region (hg38): 12:57755103-57760411

Previous symbols: [ "MARCH9" ]

Links

ENSG00000139266 ∙ NCBI:92979 ∙ OMIM:613336 ∙ HGNC:25139 ∙ Uniprot:Q86YJ5 ∙ 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 MARCHF9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MARCHF9 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			37			37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	0	0

Variants in MARCHF9

This is a list of pathogenic ClinVar variants found in the MARCHF9 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57755548-G-T		not specified	Uncertain significance (Jul 02, 2024)
12-57755557-T-C		not specified	Uncertain significance (Jul 25, 2023)
12-57755601-C-G		not specified	Uncertain significance (Jul 06, 2021)
12-57755607-G-A		not specified	Uncertain significance (Oct 20, 2023)
12-57755611-C-T		not specified	Uncertain significance (Oct 06, 2024)
12-57755616-C-T		not specified	Uncertain significance (Jul 12, 2022)
12-57755625-G-A		not specified	Uncertain significance (Sep 27, 2021)
12-57755625-G-T		not specified	Uncertain significance (Aug 28, 2024)
12-57755634-G-A		not specified	Uncertain significance (Aug 02, 2023)
12-57755650-C-T		not specified	Uncertain significance (Aug 04, 2023)
12-57755662-G-A		not specified	Uncertain significance (Jul 12, 2022)
12-57755724-C-T		not specified	Uncertain significance (Apr 23, 2024)
12-57755796-G-A		not specified	Uncertain significance (Jul 19, 2022)
12-57755808-G-C		not specified	Uncertain significance (Mar 16, 2022)
12-57755817-C-G		not specified	Uncertain significance (Aug 16, 2021)
12-57755848-C-T		not specified	Uncertain significance (Nov 09, 2024)
12-57755854-A-G		not specified	Uncertain significance (Oct 14, 2023)
12-57756932-G-C		not specified	Uncertain significance (Oct 04, 2024)
12-57756975-C-T		not specified	Uncertain significance (Feb 28, 2023)
12-57758246-C-G		not specified	Uncertain significance (Oct 03, 2022)
12-57758584-C-T		not specified	Uncertain significance (Dec 07, 2023)
12-57758668-G-A		not specified	Uncertain significance (Jun 26, 2024)
12-57758677-C-G		not specified	Uncertain significance (Jan 30, 2024)
12-57758718-C-G		not specified	Uncertain significance (Jun 03, 2024)
12-57758718-C-T		not specified	Uncertain significance (Jun 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MARCHF9	protein_coding	protein_coding	ENST00000266643	4	5310

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.731	0.269	125730	0	6	125736	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	112	162	0.691	0.00000974	2137
Missense in Polyphen		35	72.002	0.4861		907
Synonymous	2.01	45	65.8	0.684	0.00000374	744
Loss of Function	2.83	2	13.0	0.153	6.61e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000151
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000187	0.0000176
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 may mediate ubiquitination of MHC-I, CD4 and ICAM1, 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, ECO:0000269|PubMed:17174307}.

Recessive Scores

• pRec: 0.112

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.490
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.540

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: March9
• Phenotype: growth/size/body region phenotype; skeleton phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

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