SCLT1

Chr 4

sodium channel and clathrin linker 1

Also known as: CAP-1A, CAP1A

NCBI Gene: 132320ENSG00000151466UniProt: Q96NL6

This gene encodes an adapter protein that links the SCN10A sodium channel to clathrin and regulates channel activity, and also functions as a component of centriole distal appendages necessary for ciliogenesis. Mutations cause autosomal recessive intellectual disability with seizures and language delay. The gene is extremely intolerant to loss-of-function variants, indicating it is highly constrained and critical for normal development.

Summary from RefSeq, UniProt
Research Assistant →
1
Active trials
5
Pubs (1 yr)
67
P/LP submissions
2%
P/LP missense
0.89
LOEUF
DN
Mechanism· predicted
Clinical Summary— SCLT1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
62 unique Pathogenic / Likely Pathogenic· 231 VUS of 500 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — SCLT1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.89LOEUF
pLI 0.000
Z-score 2.18
OE 0.66 (0.50–0.89)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.27Z-score
OE missense 1.04 (0.95–1.14)
341 obs / 327.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.66 (0.50–0.89)
0≤0.351.4
Missense OE1.04 (0.95–1.14)
0≤0.61.4
Synonymous OE1.09
0≤1.21.6
LoF obs/exp: 32 / 48.4Missense obs/exp: 341 / 327.3Syn Z: -0.71
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
limitedSCLT1-related retinitis pigmentosaOTHERAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.74top 25%
GOF
0.6346th %ile
LOF
0.2775th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

500 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic46
Likely Pathogenic16
VUS231
Likely Benign151
Benign26
Conflicting8
46
Pathogenic
16
Likely Pathogenic
231
VUS
151
Likely Benign
26
Benign
8
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
13
0
33
0
46
Likely Pathogenic
13
1
2
0
16
VUS
4
198
29
0
231
Likely Benign
1
3
72
75
151
Benign
0
6
9
11
26
Conflicting
—8
Total3120814586478

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SCLT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients