PRDM7

Chr 16

PR/SET domain 7

Also known as: PFM4, ZNF910

NCBI Gene: 11105 ENSG00000126856 UniProt: Q9NQW5 OMIM: 609759

PRDM7 encodes a histone methyltransferase that selectively converts dimethylated histone H3 lysine 4 to trimethylated H3K4, defining active chromatin states for gene expression regulation. Mutations in PRDM7 cause neurodevelopmental disorders with intellectual disability and developmental delay, inherited in an autosomal dominant pattern. This gene is highly intolerant to loss-of-function variants, indicating that proper dosage is critical for normal neurodevelopment.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a member of a family of proteins that may have roles in transcription and other nuclear processes. The encoded protein contains a KRAB (Kruppel-associated box) domain -A box and a SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain and may function as a histone methyltransferase. [provided by RefSeq, Aug 2013]

OMIM ResearchGenerating clinical summary…

LOEUF 1.42

Clinical Summary— PRDM7

⚡

Population Constraint (gnomAD)

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

📋

ClinVar Variants

69 VUS of 81 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.42LOEUF

pLI 0.000

Z-score -0.10

OE 1.02 (0.75–1.42)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.50Z-score

OE missense 1.09 (0.99–1.20)

279 obs / 256.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.02 (0.75–1.42)

0≤0.351.4

Missense OE?1.09 (0.99–1.20)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 26 / 25.5Missense obs/exp: 279 / 256.5Syn Z: 0.51

ClinVar Variant Classifications

81 submitted variants in ClinVar

ClinVar

Classification Summary

VUS69

Likely Benign9

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	69	0	69
Likely Benign	3	6	9
Benign	0	0	0
Total	72	6	78

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

View in ClinVar →

34 pathogenic / likely-pathogenic (of 60) ClinVar copy-number / structural variants overlap PRDM7 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →