SNX22

Chr 15

sorting nexin 22

NCBI Gene: 79856 ENSG00000157734 UniProt: Q96L94

The protein encoded by this gene is a sorting nexin that is found in the cytoplasm, where it interacts with membrane-bound phosphatidylinositol 3-phosphate. The encoded protein may play a role in intracellular trafficking. Two transcript variants, one protein-coding and the other not protein-coding, have been found for this gene. [provided by RefSeq, Dec 2012]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.09

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?

1.09LOEUF

pLI 0.005

Z-score 1.38

OE 0.52 (0.27–1.09)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.02Z-score

OE missense 1.01 (0.85–1.19)

101 obs / 100.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.52 (0.27–1.09)

0≤0.351.4

Missense OE?1.01 (0.85–1.19)

0≤0.61.4

Synonymous OE?1.08

0≤1.21.6

LoF obs/exp: 5 / 9.6Missense obs/exp: 101 / 100.5Syn Z: -0.43

Background carrier burden — how many people carry a rare variant somewhere in SNX22?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 240

282 rare PASS variants

Rare truncating (LoF)

1 in 2,300

64 rare PASS variants

Rare synonymous (reference)

1 in 210

105 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SNX22. 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 330	1 in 2,500
South Asian	~43k	1 in 180	1 in 3,100
Remaining (unassigned)	~30k	1 in 180	1 in 1,000
European (Finnish)	~27k	1 in 560	≈ 1 in 6,000
Admixed American	~22k	1 in 190	1 in 3,600
African / African American	~21k	1 in 290	≈ 1 in 4,500
East Asian	~20k	1 in 250	1 in 780
Ashkenazi Jewish	~13k	1 in 590	none seen
Middle Eastern	~2,884	1 in 170	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): 6 of 7 coding exons well covered in gnomAD exomes; exon 2 marginal. Genomes: all 7.? see exons ↓