JMJD7

Chr 15

jumonji domain containing 7

NCBI Gene: 100137047 ENSG00000243789 UniProt: P0C870 OMIM: 621306

This gene encodes a highly conserved protein with a JmjC domain, which are part of the cupin metalloenzyme superfamily. JmjC proteins may function as 2-oxoglutarate-Fe(II)-dependent dioxygenases. Most tissues also express read-through transcripts from this gene into the downstream phospholipase A2, group IVB (cytosolic) gene, some of which may encode fusion proteins combining the N-terminus of this protein with the phospholipase A2, group IVB protein. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.97

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.97LOEUF

pLI 0.000

Z-score 1.67

OE 0.55 (0.33–0.97)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.92Z-score

OE missense 1.19 (1.06–1.32)

228 obs / 192.1 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.55 (0.33–0.97)

0≤0.351.4

Missense OE?1.19 (1.06–1.32)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 9 / 16.3Missense obs/exp: 228 / 192.1Syn Z: 0.01

Background carrier burden — how many people carry a rare variant somewhere in JMJD7?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 78

502 rare PASS variants

Rare truncating (LoF)

1 in 1,700

92 rare PASS variants

Rare synonymous (reference)

1 in 120

214 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for JMJD7. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 150	1 in 1,900
South Asian	~43k	1 in 79	1 in 2,400
Remaining (unassigned)	~30k	1 in 78	1 in 1,100
European (Finnish)	~27k	1 in 1,200	≈ 1 in 22,000
Admixed American	~22k	1 in 94	1 in 1,700
African / African American	~21k	1 in 99	1 in 890
East Asian	~20k	1 in 61	1 in 570
Ashkenazi Jewish	~13k	1 in 340	none seen
Middle Eastern	~2,884	1 in 99	≈ 1 in 720

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 7 of 8 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 8.? see exons ↓