IGSF11

Chr 3

immunoglobulin superfamily member 11

Also known as: BT-IgSF, BTIGSF, CT119, CXADRL1, Igsf13, VSIG3

NCBI Gene: 152404 ENSG00000144847 UniProt: Q5DX21 OMIM: 608351

IGSF11 is an immunoglobulin (Ig) superfamily member that is preferentially expressed in brain and testis. It shares significant homology with coxsackievirus and adenovirus receptor (CXADR; MIM 602621) and endothelial cell-selective adhesion molecule (ESAM).[supplied by OMIM, Apr 2005]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.79

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.79LOEUF

pLI 0.001

Z-score 2.24

OE 0.44 (0.25–0.79)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.21Z-score

OE missense 0.78 (0.69–0.88)

184 obs / 236.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.44 (0.25–0.79)

0≤0.351.4

Missense OE?0.78 (0.69–0.88)

0≤0.61.4

Synonymous OE?1.17

0≤1.21.6

LoF obs/exp: 8 / 18.4Missense obs/exp: 184 / 236.3Syn Z: -1.26

Background carrier burden — how many people carry a rare variant somewhere in IGSF11?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 97

496 rare PASS variants

Rare truncating (LoF)

1 in 2,600

68 rare PASS variants

Rare synonymous (reference)

1 in 250

231 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for IGSF11. 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 120	1 in 2,500
South Asian	~43k	1 in 100	1 in 6,100
Remaining (unassigned)	~30k	1 in 110	1 in 3,300
European (Finnish)	~27k	1 in 450	1 in 1,400
Admixed American	~22k	1 in 140	1 in 3,700
African / African American	~21k	1 in 130	1 in 2,500
East Asian	~20k	1 in 120	1 in 2,500
Ashkenazi Jewish	~13k	1 in 2,100	≈ 1 in 4,300
Middle Eastern	~2,884	1 in 110	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): All 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓