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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SCLT1
sodium channel and clathrin linker 1
Chromosome 4 Β· 4q28.2
NCBI Gene: 132320Ensembl: ENSG00000151466.12HGNC: HGNC:26406UniProt: A0A494C0G8
38PubMed Papers
20Diseases
0Drugs
52Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cilium assemblycentriolecentrosomeciliary basal bodyorofaciodigital syndrome IXRetinal dystrophySjogren-Larsson syndromeBardet-Biedl syndrome
✦AI Summary

SCLT1 (sodium channel and clathrin linker 1) is a centriole distal appendage protein essential for primary cilium assembly and function. SCLT1 functions as a structural component of the distal appendage, operating within a CEP83-SCLT1 protein module critical for anchoring the mother centriole to the cell membrane and recruiting preciliary vesicles 1. It plays a primary role in ciliary assembly rather than disassembly, with depletion severely compromising all four key steps of ciliogenesis including intraflagellar transport initiation and CP110 removal 12. Loss of SCLT1 results in reduced ciliogenesis and impaired hedgehog signaling, particularly affecting limb bud development in a tissue-specific manner 3. Disorders of SCLT1 manifest across multiple ciliopathy phenotypes. Homozygous SCLT1 variants cause oral-facial-digital syndrome, Bardet-Biedl syndrome, and Senior-LΓΈken syndrome, presenting with cystic kidney, cleft palate, polydactyly, and retinal degeneration 456. Sclt1-deficient mice develop cystic kidneys through activation of ERK and STAT3 signaling pathways, with STAT3 inhibition offering potential therapeutic benefit 4. Recent evidence extends SCLT1 involvement to nonsyndromic orofacial clefts through dominant pathogenic variants 7. The wide clinical spectrum reflects SCLT1's fundamental role in ciliary dynamics essential for developmental signaling and tissue homeostasis.

Sources cited
1
SCLT1 functions as part of the CEP83-SCLT1 module critical for distal appendage assembly and regulates preciliary vesicle recruitment, intraflagellar transport initiation, and CP110 removal
PMID: 39882846
2
SCLT1 is essential for ciliary assembly and centriole docking, representing a functional subgroup distinct from disassembly-regulating distal appendage proteins
PMID: 39696441
3
SCLT1 mutations cause tissue-specific defects in limb development and ciliogenesis through impaired distal appendage recruitment and disrupted hedgehog signaling
PMID: 36407107
4
Sclt1 deficiency causes cystic kidney disease through activation of ERK and STAT3 signaling pathways, with STAT3 inhibition reducing cyst formation
PMID: 28486600
5
SCLT1 variants are associated with Bardet-Biedl syndrome and related ciliopathies
PMID: 32055034
6
Homozygous SCLT1 mutations cause reduced cone photoreceptor function and manifestations including ADHD, obesity, and retinal degeneration
PMID: 37246745
7
Dominant SCLT1 variants contribute to nonsyndromic orofacial clefts pathogenesis
PMID: 40147726
8
SCLT1 is confirmed as a disease gene candidate associated with Mendelian phenotypes through autozygome analysis
PMID: 30237576
Disease Associationsβ“˜20
orofaciodigital syndrome IXOpen Targets
0.54Moderate
Retinal dystrophyOpen Targets
0.47Moderate
Sjogren-Larsson syndromeOpen Targets
0.47Moderate
Bardet-Biedl syndromeOpen Targets
0.44Moderate
AstigmatismOpen Targets
0.41Moderate
congenital hypothalamic hamartoma syndromeOpen Targets
0.41Moderate
Global developmental delayOpen Targets
0.41Moderate
HypermetropiaOpen Targets
0.41Moderate
NystagmusOpen Targets
0.41Moderate
OpsoclonusOpen Targets
0.41Moderate
Fetal anomalyOpen Targets
0.37Weak
smoking initiationOpen Targets
0.28Weak
skin agingOpen Targets
0.27Weak
tooth diseaseOpen Targets
0.27Weak
neurodegenerative diseaseOpen Targets
0.25Weak
mathematical abilityOpen Targets
0.24Weak
osteoarthritisOpen Targets
0.24Weak
osteoarthritis, kneeOpen Targets
0.22Weak
amyotrophic lateral sclerosisOpen Targets
0.21Weak
adolescent idiopathic scoliosisOpen Targets
0.21Weak
Pathogenic Variants52
NM_144643.4(SCLT1):c.1631A>G (p.Lys544Arg)Pathogenic
not provided|Retinal dystrophy
β˜…β˜…β˜†β˜†2025β†’ Residue 544
NM_144643.4(SCLT1):c.290+2T>CPathogenic
not provided|not specified
β˜…β˜…β˜†β˜†2024
NM_144643.4(SCLT1):c.538C>T (p.Gln180Ter)Pathogenic
not provided|SCLT1-related disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 180
NM_144643.4(SCLT1):c.37C>T (p.Arg13Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 13
NM_144643.4(SCLT1):c.1249C>T (p.Arg417Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 417
NM_144643.4(SCLT1):c.1269dup (p.Ala424fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 424
NM_144643.4(SCLT1):c.1057G>T (p.Glu353Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 353
NM_144643.4(SCLT1):c.673C>T (p.Arg225Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 225
NM_144643.4(SCLT1):c.412C>T (p.Gln138Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 138
NM_144643.4(SCLT1):c.660_661insT (p.Ile221fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 221
NM_144643.4(SCLT1):c.1830-2A>GLikely pathogenic
not provided|Uterine corpus endometrial carcinoma
β˜…β˜†β˜†β˜†2025
NM_144643.4(SCLT1):c.832C>T (p.Gln278Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 278
NM_144643.4(SCLT1):c.400C>T (p.Gln134Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 134
NM_144643.4(SCLT1):c.1439+5G>TLikely pathogenic
Retinal dystrophy
β˜…β˜†β˜†β˜†2025
NM_144643.4(SCLT1):c.778_780delLikely pathogenic
Retinal dystrophy
β˜…β˜†β˜†β˜†2025
NM_144643.4(SCLT1):c.35-1G>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_144643.4(SCLT1):c.1843C>T (p.Arg615Ter)Pathogenic
SCLT1-related disorder|not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 615
NM_144643.4(SCLT1):c.1908+1G>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_144643.4(SCLT1):c.478del (p.Arg160fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 160
NM_144643.4(SCLT1):c.1876C>T (p.Gln626Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 626
View on ClinVar β†—
Related Genes
ODF2Protein interaction100%C2CD3Protein interaction100%NINProtein interaction100%SCN10AProtein interaction89%KIZProtein interaction84%CLTCProtein interaction79%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
25%
Lung
23%
Heart
22%
Brain
18%
Liver
13%
Gene Interaction Network
Click a node to explore
SCLT1ODF2C2CD3NINSCN10AKIZCLTC
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q96NL6
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
1.10LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.66 [0.42–1.10]
RankingsWhere SCLT1 stands among ~20K protein-coding genes
  • #10,539of 20,598
    Most Researched38
  • #1,300of 5,498
    Most Pathogenic Variants52 Β· top quartile
  • #11,211of 17,882
    Most Constrained (LOEUF)1.10
Genes detectedSCLT1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
PMID: 20301537
1.00
2
Autozygome and high throughput confirmation of disease genes candidacy.
PMID: 30237576
Genet Med Β· 2019
0.90
3
The morbid genome of ciliopathies: an update.
PMID: 32055034
Genet Med Β· 2020
0.80
4
A hierarchical pathway for assembly of the distal appendages that organize primary cilia.
PMID: 39882846
Elife Β· 2025
0.70
5
Distinct roles of centriole distal appendage proteins in ciliary assembly and disassembly.
PMID: 39696441
Cell Commun Signal Β· 2024
0.60