STOML2

Chr 9

stomatin like 2

Also known as: HSPC108, SLP-2

NCBI Gene: 30968 ENSG00000165283 UniProt: Q9UJZ1 OMIM: 608292

The STOML2 protein regulates mitochondrial biogenesis and organization, stimulates cardiolipin biosynthesis, and plays roles in calcium homeostasis, T-cell activation, and cellular stress responses. Mutations cause autosomal recessive mitochondrial disorders affecting multiple systems including immune function and cellular energy metabolism. This gene is moderately constrained against loss-of-function variants, suggesting that complete loss of protein function is not well tolerated.

OMIM ResearchSummary from RefSeq, UniProt

Enables GTPase binding activity; T cell receptor binding activity; and cardiolipin binding activity. Involved in intracellular calcium ion homeostasis; mitochondrion organization; and protein complex oligomerization. Acts upstream of or within T cell receptor signaling pathway. Located in several cellular components, including immunological synapse; membrane raft; and mitochondrial envelope. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.70

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.70LOEUF

pLI 0.002

Z-score 2.59

OE 0.39 (0.23–0.70)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.55Z-score

OE missense 0.70 (0.61–0.80)

148 obs / 211.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.39 (0.23–0.70)

0≤0.351.4

Missense OE?0.70 (0.61–0.80)

0≤0.61.4

Synonymous OE?1.07

0≤1.21.6

LoF obs/exp: 8 / 20.7Missense obs/exp: 148 / 211.2Syn Z: -0.48

Background carrier burden — how many people carry a rare variant somewhere in STOML2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 220

381 rare PASS variants

Rare truncating (LoF)

1 in 8,200

48 rare PASS variants

Rare synonymous (reference)

1 in 220

192 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for STOML2. 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 220	1 in 10,000
South Asian	~43k	1 in 340	1 in 4,300
Remaining (unassigned)	~30k	1 in 160	≈ 1 in 7,500
European (Finnish)	~27k	1 in 490	1 in 4,400
Admixed American	~22k	1 in 160	≈ 1 in 11,000
African / African American	~21k	1 in 280	1 in 2,400
East Asian	~20k	1 in 200	none seen
Ashkenazi Jewish	~13k	1 in 1,200	≈ 1 in 6,500
Middle Eastern	~2,884	≈ 1 in 720	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 10 coding exons well covered in gnomAD exomes and genomes.? see exons ↓