LRCH3

Chr 3

leucine rich repeats and calponin homology domain containing 3

NCBI Gene: 84859 ENSG00000186001 UniProt: Q96II8

Involved in septin cytoskeleton organization. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

Research

Involved in septin cytoskeleton organization. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.81

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?

0.81LOEUF

pLI 0.000

Z-score 2.54

OE 0.58 (0.42–0.81)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.28Z-score

OE missense 0.96 (0.88–1.05)

371 obs / 386.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.58 (0.42–0.81)

0≤0.351.4

Missense OE?0.96 (0.88–1.05)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 25 / 43.0Missense obs/exp: 371 / 386.4Syn Z: 0.30

Background carrier burden — how many people carry a rare variant somewhere in LRCH3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 50

1,095 rare PASS variants

Rare truncating (LoF)

1 in 660

181 rare PASS variants

Rare synonymous (reference)

1 in 120

402 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for LRCH3. 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 83	1 in 640
South Asian	~43k	1 in 48	1 in 870
Remaining (unassigned)	~30k	1 in 48	1 in 810
European (Finnish)	~27k	1 in 120	1 in 3,800
Admixed American	~22k	1 in 55	1 in 520
African / African American	~21k	1 in 48	1 in 1,300
East Asian	~20k	1 in 54	1 in 870
Ashkenazi Jewish	~13k	1 in 370	1 in 2,200
Middle Eastern	~2,884	1 in 46	≈ 1 in 720

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): 17 of 21 coding exons well covered in gnomAD exomes; exons 2, 4, 10, 16 marginal. Genomes: 20 of 21 (exon 3 below).? see exons ↓