LY75-CD302

Chr 2

LY75-CD302 readthrough

Also known as: gp200-MR6

This locus represents naturally occurring read-through transcription between the neighboring lymphocyte antigen 75 (LY75) and CD302 molecule (CD302) genes. Alternative splicing results in multiple transcript variants encoding fusion products that share sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.93

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.93LOEUF

pLI 0.000

Z-score 2.20

OE 0.77 (0.65–0.93)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.02Z-score

OE missense 1.00 (0.95–1.06)

963 obs / 961.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.77 (0.65–0.93)

0≤0.351.4

Missense OE?1.00 (0.95–1.06)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 84 / 108.7Missense obs/exp: 963 / 961.5Syn Z: 0.98

Background carrier burden — how many people carry a rare variant somewhere in LY75-CD302?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 30

2,285 rare PASS variants

Rare truncating (LoF)

1 in 200

445 rare PASS variants

Rare synonymous (reference)

1 in 65

750 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for LY75-CD302. 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 36	1 in 260
South Asian	~43k	1 in 27	1 in 170
Remaining (unassigned)	~30k	1 in 23	1 in 130
European (Finnish)	~27k	1 in 57	1 in 1,500
Admixed American	~22k	1 in 22	1 in 150
African / African American	~21k	1 in 23	1 in 300
East Asian	~20k	1 in 26	1 in 140
Ashkenazi Jewish	~13k	1 in 120	1 in 1,400
Middle Eastern	~2,884	1 in 21	1 in 170

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 37 of 39 coding exons well covered in gnomAD exomes; exon 38 poorly covered; exon 1 marginal. Genomes: all 39.? see exons ↓