ARPIN-AP3S2

Chr 15

ARPIN-AP3S2 readthrough

Also known as: C15orf38-AP3S2

This read-through transcript produces a fusion protein combining sequences from C15orf38 and AP3S2 (adaptor-related protein complex 3 sigma 2 subunit), where AP3S2 normally functions in intracellular vesicle trafficking and protein sorting. The gene shows extremely low constraint against loss-of-function variants, and no specific disease associations have been established for mutations in this fusion transcript. The clinical significance of variants in this read-through transcript remains unclear.

ResearchSummary from RefSeq

This locus represents naturally occurring read-through transcription between the neighboring C15orf38 (chromosome 15 open reading frame 38) and AP3S2 (adaptor-related protein complex 3, sigma 2 subunit) genes. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.34

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.34LOEUF

pLI 0.000

Z-score 0.41

OE 0.90 (0.62–1.34)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.15Z-score

OE missense 0.97 (0.87–1.08)

231 obs / 237.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.90 (0.62–1.34)

0≤0.351.4

Missense OE?0.97 (0.87–1.08)

0≤0.61.4

Synonymous OE?1.06

0≤1.21.6

LoF obs/exp: 18 / 20.0Missense obs/exp: 231 / 237.6Syn Z: -0.48

Background carrier burden — how many people carry a rare variant somewhere in ARPIN-AP3S2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 88

559 rare PASS variants

Rare truncating (LoF)

1 in 1,600

102 rare PASS variants

Rare synonymous (reference)

1 in 130

219 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ARPIN-AP3S2. 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 130	1 in 2,400
South Asian	~43k	1 in 80	1 in 1,300
Remaining (unassigned)	~30k	1 in 81	1 in 400
European (Finnish)	~27k	1 in 200	1 in 1,000
Admixed American	~22k	1 in 88	1 in 740
African / African American	~21k	1 in 78	1 in 870
East Asian	~20k	1 in 89	1 in 820
Ashkenazi Jewish	~13k	1 in 410	none seen
Middle Eastern	~2,884	1 in 78	≈ 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): 9 of 10 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 10.? see exons ↓