ARL2-SNX15

Chr 11

ARL2-SNX15 readthrough (NMD candidate)

This locus represents naturally occurring read-through transcription between the neighboring ADP-ribosylation factor-like 2 (ARL2) and sorting nexin 15 (SNX15) genes on chromosome 11. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

—

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in ARL2-SNX15?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 400

134 rare PASS variants

Rare truncating (LoF)

1 in 7,300

23 rare PASS variants

Rare synonymous (reference)

1 in 1,400

71 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ARL2-SNX15. 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 760	1 in 6,500
South Asian	~43k	1 in 590	≈ 1 in 22,000
Remaining (unassigned)	~30k	1 in 440	1 in 4,900
European (Finnish)	~27k	1 in 3,300	≈ 1 in 26,000
Admixed American	~22k	1 in 800	≈ 1 in 22,000
African / African American	~21k	1 in 1,100	≈ 1 in 8,400
East Asian	~20k	1 in 300	≈ 1 in 9,900
Ashkenazi Jewish	~13k	1 in 690	none seen
Middle Eastern	~2,884	1 in 480	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): 3 of 4 coding exons well covered in gnomAD exomes; exon 4 poorly covered. Genomes: all 4.? see exons ↓