MARF1

meiosis regulator and mRNA stability factor 1, the group of MicroRNA protein coding host genes|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 16:15594386-15643154

Previous symbols: [ "KIAA0430" ]

Links

ENSG00000166783 ∙ NCBI:9665 ∙ OMIM:614593 ∙ HGNC:29562 ∙ Uniprot:Q9Y4F3 ∙ 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 MARF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MARF1 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	2
missense			78	10		88
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	78	11	1

Variants in MARF1

This is a list of pathogenic ClinVar variants found in the MARF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-15596718-G-A		not specified	Uncertain significance (Aug 15, 2023)
16-15596788-T-C		not specified	Uncertain significance (Mar 02, 2023)
16-15596854-A-G		not specified	Likely benign (Feb 02, 2024)
16-15596880-T-C		not specified	Uncertain significance (Jun 09, 2022)
16-15596917-C-T		not specified	Uncertain significance (Sep 28, 2022)
16-15596931-A-G		not specified	Uncertain significance (Mar 18, 2024)
16-15598974-C-T		not specified	Uncertain significance (Sep 18, 2023)
16-15598986-C-T		not specified	Likely benign (Jun 24, 2022)
16-15598994-C-T		not specified	Uncertain significance (Mar 16, 2024)
16-15600469-G-A		not specified	Uncertain significance (Sep 14, 2022)
16-15600490-C-T		not specified	Uncertain significance (Dec 27, 2023)
16-15600491-G-A		not specified	Uncertain significance (Jan 27, 2022)
16-15600502-G-A		not specified	Uncertain significance (Dec 11, 2023)
16-15600520-T-C		not specified	Likely benign (Jun 29, 2023)
16-15600535-C-T		not specified	Uncertain significance (Mar 14, 2023)
16-15602020-C-T		not specified	Uncertain significance (Jan 06, 2023)
16-15602050-G-C		not specified	Uncertain significance (Aug 17, 2022)
16-15602076-G-A		not specified	Uncertain significance (May 28, 2024)
16-15602128-A-C		not specified	Uncertain significance (Mar 22, 2024)
16-15602160-C-T		not specified	Uncertain significance (Jul 08, 2022)
16-15604242-T-C		not specified	Uncertain significance (Nov 07, 2023)
16-15604359-T-G		not specified	Uncertain significance (May 03, 2023)
16-15604366-C-A		not specified	Uncertain significance (May 23, 2023)
16-15608296-C-T		not specified	Uncertain significance (May 23, 2024)
16-15608351-G-C			Benign (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MARF1	protein_coding	protein_coding	ENST00000396368	26	48781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.53e-10	124780	0	15	124795	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.73	733	973	0.754	0.0000559	11445
Missense in Polyphen		228	377.79	0.60351		4582
Synonymous	-1.59	434	394	1.10	0.0000250	3432
Loss of Function	7.64	4	75.7	0.0528	0.00000366	957

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000158	0.000158
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000531	0.0000530
Middle Eastern	0.000111	0.000111
South Asian	0.0000656	0.0000654
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential regulator of oogenesis required for female meiotic progression to repress transposable elements and preventing their mobilization, which is essential for the germline integrity. Probably acts via some RNA metabolic process, equivalent to the piRNA system in males, which mediates the repression of transposable elements during meiosis by forming complexes composed of RNAs and governs the methylation and subsequent repression of transposons. Also required to protect from DNA double-strand breaks (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -1.52
• rvis_percentile_EVS: 3.45

Haploinsufficiency Scores

• pHI: 0.136
• hipred: Y
• hipred_score: 0.728
• ghis: 0.595

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Marf1
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: double-strand break repair;female meiotic nuclear division;regulation of gene expression;negative regulation of phosphatase activity;oogenesis
• Cellular component: peroxisome;Golgi apparatus;membrane;intracellular membrane-bounded organelle
• Molecular function: molecular_function;RNA binding