SLC25A30

Chr 13

solute carrier family 25 member 30

Also known as: KMCP1

NCBI Gene: 253512 ENSG00000174032 UniProt: Q5SVS4

SLC25A30 encodes a mitochondrial carrier protein that transports inorganic anions (particularly sulfate, sulfite, thiosulfate, and phosphate) across the inner mitochondrial membrane and may regulate hydrogen sulfide levels by exporting its degradation products from mitochondria. Biallelic mutations cause progressive myoclonic epilepsy with ataxia and sensorineural hearing loss, following an autosomal recessive inheritance pattern. This gene shows minimal constraint against loss-of-function variants (pLI near zero), consistent with the recessive disease mechanism.

ResearchSummary from RefSeq, UniProt

Although the outer mitochondrial membrane is permeable to many small metabolites, transport of solutes across the inner mitochondrial membrane is achieved by members of the mitochondrial carrier protein family, such as SLC25A30 (Haguenauer et al., 2005 [PubMed 15809292]).[supplied by OMIM, Mar 2008]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.19

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.19LOEUF

pLI 0.000

Z-score 0.93

OE 0.77 (0.52–1.19)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.93Z-score

OE missense 0.80 (0.69–0.92)

134 obs / 168.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.77 (0.52–1.19)

0≤0.351.4

Missense OE?0.80 (0.69–0.92)

0≤0.61.4

Synonymous OE?0.90

0≤1.21.6

LoF obs/exp: 15 / 19.4Missense obs/exp: 134 / 168.0Syn Z: 0.63

Background carrier burden — how many people carry a rare variant somewhere in SLC25A30?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 190

325 rare PASS variants

Rare truncating (LoF)

1 in 2,100

68 rare PASS variants

Rare synonymous (reference)

1 in 630

131 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC25A30. 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 2,700
South Asian	~43k	1 in 180	1 in 1,500
Remaining (unassigned)	~30k	1 in 220	1 in 2,500
European (Finnish)	~27k	1 in 450	1 in 3,800
Admixed American	~22k	1 in 110	1 in 390
African / African American	~21k	1 in 120	1 in 2,500
East Asian	~20k	1 in 460	1 in 960
Ashkenazi Jewish	~13k	1 in 1,500	none seen
Middle Eastern	~2,884	1 in 120	≈ 1 in 2,900

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 ↓