PMF1

protein-coding

polyamine modulated factor 1, the group of MIS12 kinetochore complex

Gene summary

Enables leucine zipper domain binding activity and transcription coactivator activity. Involved in chromosome segregation. Located in kinetochore and nucleoplasm. Part of MIS12/MIND type complex. Implicated in bladder carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_007221.4

Inheritance

—

ClinVar variants

U:20B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr1:156,212,993-156,240,042

External References & Databases

Ensembl (ENSG00000160783)

Transcript & Mutation Effects

hg38 • Region Span ~27.0 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 PMF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007221.4. 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	2 clinvar		3
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	2	0	22

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007221.4	RefSeq	NP_009152.2	5	MANE Select
ENST00000368277.3	Ensembl	ENSP00000357260.3	5	MANE Select
NM_001199653.2	RefSeq	NP_001186582.1	5	Standard
NM_001199654.2	RefSeq	NP_001186583.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
Amplification of signal from the kinetochores
Mitotic Spindle Checkpoint
Cell Cycle Checkpoints

Biological Process

transcription by RNA polymerase II
cell cycle
chromosome segregation
cell division
positive regulation of nucleic acid-templated transcription

Molecular Function

transcription coactivator activity
protein binding
leucine zipper domain binding

Cellular Component

MIS12/MIND type complex
condensed chromosome kinetochore
nuclear MIS12/MIND complex
nucleoplasm
transcription factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000567140
Coding exons: 7
Length: 30091
Individuals with no LoFs: 125710
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 125748
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.346	140	129	1.09	0.00000677	1427
Missense (PolyPhen)		34	42.394	0.80199		491
Synonymous	0.0217	50	50.2	0.996	0.00000288	404
Loss of Function	0.326	13	14.3	0.907	6.97e-7	150

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000068	0.000062	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis. May act as a cotranscription partner of NFE2L2 involved in regulation of polyamine-induced transcription of SSAT. {ECO:0000269|PubMed:10419538, ECO:0000269|PubMed:11256947, ECO:0000269|PubMed:15502821, ECO:0000269|PubMed:16585270}.;

Recessive Scores

pRec: 0.262

Intolerance Scores

LoFtool: 0.697
RVIS EVS: 0.88
RVIS percentile EVS: 89.07

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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