EXOC3L2

Chr 19AR

exocyst complex component 3 like 2

Also known as: BMRS, XTP7

NCBI Gene: 90332 ENSG00000283632 UniProt: Q2M3D2 OMIM: 616927

The protein encoded by this gene is upregulated by vascular endothelial growth factor A and interacts with exocyst complex component 4. The encoded protein may be part of an exocyst complex that plays a role in cell membrane dynamics. Mutations in this gene may be associated with Alzheimer's disease. [provided by RefSeq, May 2017]

OMIM Research

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Brain malformation renal syndromeMIM #620943

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Brain malformation renal syndrome; no ClinGen or GenCC tier

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.43

LOEUF

GOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.43LOEUF

pLI 0.760

Z-score 3.26

OE 0.17 (0.07–0.43)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

0.66Z-score

OE missense 0.88 (0.79–0.99)

224 obs / 253.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.17 (0.07–0.43)

0≤0.351.4

Missense OE?0.88 (0.79–0.99)

0≤0.61.4

Synonymous OE?1.05

0≤1.21.6

LoF obs/exp: 3 / 17.9Missense obs/exp: 224 / 253.5Syn Z: -0.39

Background carrier burden — how many people carry a rare variant somewhere in EXOC3L2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 42

885 rare PASS variants

Rare truncating (LoF)

1 in 3,100

62 rare PASS variants

Rare synonymous (reference)

1 in 82

416 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for EXOC3L2. 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 48	1 in 2,900
South Asian	~43k	1 in 32	1 in 4,200
Remaining (unassigned)	~30k	1 in 34	none seen
European (Finnish)	~27k	1 in 100	≈ 1 in 6,100
Admixed American	~22k	1 in 34	1 in 550
African / African American	~21k	1 in 36	1 in 3,600
East Asian	~20k	1 in 39	1 in 1,700
Ashkenazi Jewish	~13k	1 in 180	≈ 1 in 4,600
Middle Eastern	~2,884	1 in 30	≈ 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): 8 of 11 coding exons well covered in gnomAD exomes; exons 2, 3 poorly covered; exon 10 marginal. Genomes: 10 of 11 (exon 9 below).? see exons ↓