EFCAB12

Chr 3

EF-hand calcium binding domain 12

Also known as: C3orf25

NCBI Gene: 90288 ENSG00000172771 UniProt: Q6NXP0

Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Research

Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.78

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.78LOEUF

pLI 0.000

Z-score 2.39

OE 0.48 (0.31–0.78)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.45Z-score

OE missense 0.93 (0.85–1.02)

307 obs / 329.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.48 (0.31–0.78)

0≤0.351.4

Missense OE?0.93 (0.85–1.02)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 12 / 24.9Missense obs/exp: 307 / 329.7Syn Z: 0.33

Background carrier burden — how many people carry a rare variant somewhere in EFCAB12?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 51

701 rare PASS variants

Rare truncating (LoF)

1 in 260

118 rare PASS variants

Rare synonymous (reference)

1 in 170

279 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for EFCAB12. 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 73	1 in 470
South Asian	~43k	1 in 41	1 in 540
Remaining (unassigned)	~30k	1 in 37	1 in 280
European (Finnish)	~27k	1 in 230	1 in 3,000
Admixed American	~22k	1 in 60	1 in 360
African / African American	~21k	1 in 60	1 in 390
East Asian	~20k	1 in 61	1 in 540
Ashkenazi Jewish	~13k	1 in 150	≈ 1 in 4,300
Middle Eastern	~2,884	1 in 49	1 in 410

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 9 coding exons well covered in gnomAD exomes and genomes.? see exons ↓