MAF1

protein-coding

MAF1 homolog, negative regulator of RNA polymerase III

Gene summary

This gene encodes a protein that is similar to Maf1, a Saccharomyces cerevisiae protein highly conserved in eukaryotic cells. Yeast Maf1 is a negative effector of RNA polymerase III (Pol III). It responds to changes in the cellular environment and represses pol III transcription. Biochemical studies identified the initiation factor TFIIIB as a target for Maf1-dependent repression. [provided by RefSeq, Jul 2008]

MANE transcript

NM_032272.5

Inheritance

—

ClinVar variants

U:33B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr8:144,104,420-144,107,611

External References & Databases

Ensembl (ENSG00000179632)

Transcript & Mutation Effects

hg38 • Region Span ~3.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAF1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 26

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032272.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			24 clinvar	3 clinvar		27
nonsense						0
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	33	4	0	37

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032272.5	RefSeq	NP_115648.2	7	MANE Select
ENST00000322428.10	Ensembl	ENSP00000318604.5	7	MANE Select
ENST00000527058.1	Ensembl	ENSP00000436030.1	5	Standard
ENST00000527572.5	Ensembl	ENSP00000431907.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Regulation of PTEN gene transcription
PTEN Regulation
PIP3 activates AKT signaling
Intracellular signaling by second messengers

Biological Process

negative regulation of transcription by RNA polymerase III

Molecular Function

RNA polymerase III core binding
RNA polymerase III type 1 promoter DNA binding
RNA polymerase III type 2 promoter DNA binding
RNA polymerase III type 3 promoter DNA binding
GABA receptor binding

Cellular Component

nucleus
nucleoplasm
nucleolus
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000322428
Coding exons: 7
Length: 3113
Individuals with no LoFs: 124720
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 124721
p: 0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.22	69	144	0.480	0.00000831	1704
Missense (PolyPhen)		16	47.916	0.33392		622
Synonymous	-3.25	87	56.0	1.55	0.00000351	452
Loss of Function	3.18	1	13.7	0.0728	6.74e-7	164

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Element of the mTORC1 signaling pathway that acts as a mediator of diverse signals and that represses RNA polymerase III transcription. Inhibits the de novo assembly of TFIIIB onto DNA. {ECO:0000269|PubMed:20233713, ECO:0000269|PubMed:20516213, ECO:0000269|PubMed:20543138}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.288
RVIS EVS: -0.12
RVIS percentile EVS: 44.89

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.985

Gene Damage Prediction

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