CTXN2

Chr 15

cortexin 2

NCBI Gene: 399697 ENSG00000233932 UniProt: P0C2S0

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Research

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.80

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?

1.80LOEUF

pLI 0.035

Z-score 0.35

OE 0.77 (0.30–1.80)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.98Z-score

OE missense 0.57 (0.41–0.81)

24 obs / 41.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.77 (0.30–1.80)

0≤0.351.4

Missense OE?0.57 (0.41–0.81)

0≤0.61.4

Synonymous OE?0.80

0≤1.21.6

LoF obs/exp: 2 / 2.6Missense obs/exp: 24 / 41.8Syn Z: 0.65

Background carrier burden — how many people carry a rare variant somewhere in CTXN2?

gnomAD v4 · ~700k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 650

95 rare PASS variants

Rare truncating (LoF)

1 in 13,000

14 rare PASS variants

Rare synonymous (reference)

1 in 1,100

43 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CTXN2. 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)	~539k	1 in 720	1 in 11,000
South Asian	~40k	1 in 740	≈ 1 in 13,000
Remaining (unassigned)	~29k	1 in 370	none seen
European (Finnish)	~25k	1 in 800	≈ 1 in 12,000
African / African American	~21k	1 in 520	none seen
East Asian	~18k	1 in 340	≈ 1 in 18,000
Admixed American	~18k	1 in 680	≈ 1 in 8,900
Ashkenazi Jewish	~13k	≈ 1 in 6,300	≈ 1 in 13,000
Middle Eastern	~2,849	≈ 1 in 950	≈ 1 in 2,800

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 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓