SLAIN1

Chr 13

SLAIN family member 1

Also known as: C13orf32

NCBI Gene: 122060 ENSG00000139737 UniProt: Q8ND83

The protein is a microtubule plus-end tracking protein that regulates cytoplasmic microtubule dynamics, organization, and elongation. Mutations cause autosomal recessive developmental and epileptic encephalopathy with microcephaly, typically presenting in infancy with seizures and developmental delay. The gene is highly constrained against loss-of-function mutations (pLI 0.90, LOEUF 0.38), indicating that complete loss of protein function is poorly tolerated.

ResearchSummary from RefSeq, UniProt

Predicted to be involved in cytoplasmic microtubule organization; microtubule nucleation; and positive regulation of microtubule polymerization. Predicted to be located in microtubule plus-end. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Clinical highlights

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

0.38

LOEUF

LOF

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

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.38LOEUF

pLI 0.901

Z-score 3.60

OE 0.15 (0.07–0.38)

Highly constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.22Z-score

OE missense 0.78 (0.69–0.88)

183 obs / 235.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.15 (0.07–0.38)

0≤0.351.4

Missense OE?0.78 (0.69–0.88)

0≤0.61.4

Synonymous OE?1.05

0≤1.21.6

LoF obs/exp: 3 / 20.7Missense obs/exp: 183 / 235.9Syn Z: -0.41

Background carrier burden — how many people carry a rare variant somewhere in SLAIN1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 87

875 rare PASS variants

Rare truncating (LoF)

1 in 1,600

89 rare PASS variants

Rare synonymous (reference)

1 in 150

420 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLAIN1. 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 130	1 in 1,500
South Asian	~43k	1 in 50	1 in 1,400
Remaining (unassigned)	~30k	1 in 64	1 in 1,300
European (Finnish)	~27k	1 in 270	1 in 4,300
Admixed American	~22k	1 in 69	1 in 850
African / African American	~21k	1 in 70	1 in 970
East Asian	~20k	1 in 88	1 in 1,300
Ashkenazi Jewish	~13k	1 in 420	≈ 1 in 3,400
Middle Eastern	~2,884	1 in 54	1 in 550

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): 6 of 7 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 7.? see exons ↓