ELMO2

Chr 20

engulfment and cell motility 2

Also known as: CED-12, CED12, Ced-12A, ELMO-2, VMPI

NCBI Gene: 63916 ENSG00000062598 UniProt: Q96JJ3

The protein encoded by this gene interacts with the dedicator of cyto-kinesis 1 protein. Similarity to a C. elegans protein suggests that this protein may function in phagocytosis of apoptotic cells and in cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

Research

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtVascular malformation, primary intraosseous

Clinical highlights

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.56

LOEUF

LOF

Mechanism· G2P

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Missense constrained — critical functional residues

LoF Constraint?

0.56LOEUF

pLI 0.000

Z-score 3.95

OE 0.37 (0.25–0.56)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

3.27Z-score

OE missense 0.55 (0.50–0.62)

235 obs / 424.9 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.37 (0.25–0.56)

0≤0.351.4

Missense OE?0.55 (0.50–0.62)

0≤0.61.4

Synonymous OE?1.05

0≤1.21.6

LoF obs/exp: 17 / 45.8Missense obs/exp: 235 / 424.9Syn Z: -0.45

Background carrier burden — how many people carry a rare variant somewhere in ELMO2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 170

610 rare PASS variants

Rare truncating (LoF)

1 in 3,300

64 rare PASS variants

Rare synonymous (reference)

1 in 96

347 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ELMO2. 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 250	1 in 2,900
South Asian	~43k	1 in 100	1 in 2,700
Remaining (unassigned)	~30k	1 in 130	1 in 980
European (Finnish)	~27k	1 in 170	1 in 2,900
Admixed American	~22k	1 in 150	1 in 2,500
African / African American	~21k	1 in 160	≈ 1 in 4,200
East Asian	~20k	1 in 120	≈ 1 in 4,900
Ashkenazi Jewish	~13k	1 in 510	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 170	≈ 1 in 1,400

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