DIPK2A

Chr 3

divergent protein kinase domain 2A

Also known as: C3orf58, DIA1, GoPro49, HASF

NCBI Gene: 205428 ENSG00000181744 UniProt: Q8NDZ4 OMIM: 612200

Involved in several processes, including cardiac muscle cell proliferation; negative regulation of smooth muscle cell apoptotic process; and positive regulation of protein kinase C activity. Located in Golgi membrane and obsolete extracellular space. Part of COPI vesicle coat. [provided by Alliance of Genome Resources, Jun 2026]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.87

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.87LOEUF

pLI 0.001

Z-score 1.96

OE 0.48 (0.28–0.87)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.03Z-score

OE missense 0.81 (0.72–0.92)

199 obs / 244.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.48 (0.28–0.87)

0≤0.351.4

Missense OE?0.81 (0.72–0.92)

0≤0.61.4

Synonymous OE?1.09

0≤1.21.6

LoF obs/exp: 8 / 16.6Missense obs/exp: 199 / 244.4Syn Z: -0.71

Background carrier burden — how many people carry a rare variant somewhere in DIPK2A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 180

618 rare PASS variants

Rare truncating (LoF)

1 in 2,700

81 rare PASS variants

Rare synonymous (reference)

1 in 120

342 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for DIPK2A. 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 230	1 in 2,400
South Asian	~43k	1 in 120	1 in 3,500
Remaining (unassigned)	~30k	1 in 160	1 in 4,200
European (Finnish)	~27k	1 in 540	≈ 1 in 11,000
Admixed American	~22k	1 in 160	≈ 1 in 8,800
African / African American	~21k	1 in 230	1 in 2,800
East Asian	~20k	1 in 110	1 in 730
Ashkenazi Jewish	~13k	1 in 720	1 in 1,100
Middle Eastern	~2,884	1 in 120	none seen

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): All 3 coding exons well covered in gnomAD exomes and genomes.? see exons ↓