PDE4DIP

Chr 1

phosphodiesterase 4D interacting protein

Also known as: CMYA2, MMGL

NCBI Gene: 9659 ENSG00000178104 UniProt: Q5VU43 OMIM: 608117

The protein encoded by this gene serves to anchor phosphodiesterase 4D to the Golgi/centrosome region of the cell. Defects in this gene may be a cause of myeloproliferative disorder (MBD) associated with eosinophilia. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2010]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.82

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.82LOEUF

pLI 0.000

Z-score 3.13

OE 0.68 (0.56–0.82)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-1.40Z-score

OE missense 1.12 (1.07–1.18)

1136 obs / 1010.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.68 (0.56–0.82)

0≤0.351.4

Missense OE?1.12 (1.07–1.18)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 76 / 111.7Missense obs/exp: 1136 / 1010.5Syn Z: 0.27

Background carrier burden — how many people carry a rare variant somewhere in PDE4DIP?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 22

1,562 rare PASS variants

Rare truncating (LoF)

1 in 190

190 rare PASS variants

Rare synonymous (reference)

1 in 39

625 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PDE4DIP. 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 25	1 in 160
South Asian	~43k	1 in 18	1 in 290
Remaining (unassigned)	~30k	1 in 20	1 in 580
European (Finnish)	~27k	1 in 59	1 in 260
Admixed American	~22k	1 in 23	1 in 250
African / African American	~21k	1 in 18	1 in 300
East Asian	~20k	1 in 23	1 in 200
Ashkenazi Jewish	~13k	1 in 73	1 in 520
Middle Eastern	~2,884	1 in 23	≈ 1 in 660

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 47 coding exons well covered in gnomAD exomes; exons 1, 2, 3, 4, 7 and 17 more poorly covered; exons 5, 6, 10, 11, 14 and 13 more marginal. Genomes: 15 of 47 (exons 1, 2, 3, 4, 6 and 27 more below).? see exons ↓