PMF1

Chr 1

polyamine modulated factor 1

NCBI Gene: 11243 ENSG00000160783 UniProt: Q6P1K2 OMIM: 609176

Enables leucine zipper domain binding activity and transcription coactivator activity. Involved in chromosome segregation. Located in Golgi apparatus; kinetochore; and nucleoplasm. Part of MIS12/MIND type complex. Implicated in bladder carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

GOFmechanismLOEUF 1.44

Clinical Summary— PMF1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

27 VUS of 32 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.44LOEUF

pLI 0.000

Z-score 0.33

OE 0.91 (0.59–1.44)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.35Z-score

OE missense 1.09 (0.95–1.25)

140 obs / 128.9 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.91 (0.59–1.44)

0≤0.351.4

Missense OE?1.09 (0.95–1.25)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 13 / 14.3Missense obs/exp: 140 / 128.9Syn Z: 0.02

This gene — mechanism propensity

0.6064th %ile

GOF

0.6736th %ile

LOF

0.3261th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

32 submitted variants in ClinVar

ClinVar

Classification Summary

VUS27

Likely Benign3

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	27	0	27
Likely Benign	2	1	3
Benign	0	0	0
Total	29	1	30

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

19 pathogenic / likely-pathogenic (of 31) ClinVar copy-number / structural variants overlap PMF1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →