SCLT1 (sodium channel and clathrin linker 1)

Gene

• Entrez ID: 132320
• Gene name: Sodium channel and clathrin linker 1
• Gene symbol: SCLT1
• Synonyms (NCBI Gene): CAP-1A, CAP1A
• Chromosome: 4
• Chromosome location: 4q28.2
• Summary: This gene encodes an adaptor protein. Studies of a related gene in rat suggest that the encoded protein functions to link clathrin to the sodium channel protein type 10 subunit alpha protein. The encoded protein has also been identified as a component of

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2097685	hsa-miR-3148	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	21399614
GO:0005814	Component	Centriole	IBA
GO:0005814	Component	Centriole	IDA	23348840
GO:0005814	Component	Centriole	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0017080	Function	Sodium channel regulator activity	IEA
GO:0030276	Function	Clathrin binding	IEA
GO:0036064	Component	Ciliary basal body	IDA
GO:0045162	Process	Clustering of voltage-gated sodium channels	IEA
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IMP	23348840
GO:0060271	Process	Cilium assembly	IMP	23348840
GO:0071439	Component	Clathrin complex	IEA
GO:0097539	Component	Ciliary transition fiber	IDA	23348840

Other IDs

• MIM: 611399
• HGNC: 26406
• e!Ensembl: ENSG00000151466

Protein

• UniProt ID: Q96NL6
• Protein name: Sodium channel and clathrin linker 1 (Sodium channel-associated protein 1)
• Protein function: Adapter protein that links SCN10A to clathrin. Regulates SCN10A channel activity, possibly by promoting channel internalization (By similarity).
• Sequence:

  MAAEIDFLREQNRRLNEDFRRYQMESFSKYSSVQKAVCQGEGDDTFENLVFDQSFLAPLV
  TEYDKHLGELNGQLKYYQKQVGEMKLQLENVIKENERLHSELKDAVEKKLEAFPLGTEVG
  TDIYADDETVRNLQEQLQLANQEKTQAVELWQTVSQELDRLHKLYQEHMTEAQIHVFESQ
  KQKDQLFDFQQLTKQLHVTNENMEVTNQQFLKTVTEQSVIIEQLRKKLRQAKLELRVAVA
  KVEELTNVTEDLQGQMKKKEKDVVSAHGREEASDRRLQQLQSSIKQLEIRLCVTIQEANQ
  LRTENTHLEKQTRELQAKCNELENERYEAIVRARNSMQLLEEANLQKSQALLEEKQKEED
  IEKMKETVSRFVQDATIRTKKEVANTKKQCNIQISRLTEELSALQMECAEKQGQIERVIK
  EKKAVEEELEKIYREGRGNESDYRKLEEMHQRFLVSERSKDDLQLRLTRAENRIKQLETD
  SSEEISRYQEMIQKLQNVLESERENCGLVSEQRLKLQQENKQLRKETESLRKIALEAQKK
  AKVKISTMEHEFSIKERGFEVQLREMEDSNRNSIVELRHLLATQQKAANRWKEETKKLTE
  SAEIRINNLKSELSRQKLHTQELLSQLEMANEKVAENEKLILEHQEKANRLQRRLSQAEE
  RAASASQQLSVITVQRRKAASLMNLENI

• Sequence length: 688

Pathways

Reactome:

Anchoring of the basal body to the plasma membrane

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Ovarian serous cystadenocarcinoma	Likely pathogenic	rs779357435	RCV005934648	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SCLT1-related disorder	Pathogenic	rs1743299340	RCV005253947	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Uterine corpus endometrial carcinoma	Likely pathogenic	rs770099403	RCV005928558	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTIGMATISM	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARDET-BIEDL SYNDROME	—	CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CILIOPATHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONE-ROD DYSTROPHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Esophageal atresia/tracheoesophageal fistula	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLOBAL DEVELOPMENTAL DELAY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPEROPIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NYSTAGMUS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
OROFACIODIGITAL SYNDROME 9	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome IX	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal dystrophy	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENIOR-LOKEN SYNDROME	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
alpha-Thalassemia	alpha Thalassemia	BEFREE	17900295		★☆☆☆☆ Found in Text Mining only
alpha^+^ Thalassemia	alpha Thalassemia	BEFREE	17900295		★☆☆☆☆ Found in Text Mining only
beta Thalassemia	beta Thalassemia	BEFREE	17900295		★☆☆☆☆ Found in Text Mining only
beta^+^ Thalassemia	beta Thalassemia	BEFREE	17900295		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	26474971	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	37185598	Associate	★☆☆☆☆ Found in Text Mining only
Chronic Obstructive Airway Disease	Chronic Obstructive Pulmonary Disease	GWASCAT_DG	24621683		★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	BEFREE	24285566, 24882706, 28486600, 30425282		★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathy	Pubtator	24882706, 32055034, 37246745	Associate	★☆☆☆☆ Found in Text Mining only
Colitis	Colitis	BEFREE	26195794		★☆☆☆☆ Found in Text Mining only
Cystic kidney	Cystic Kidney Disease	BEFREE	28486600		★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty liver	Pubtator	33132306	Associate	★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	Pubtator	32253632	Associate	★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	26195794		★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	32253632	Associate	★☆☆☆☆ Found in Text Mining only
Leukodystrophy, Metachromatic	Metachromatic Leukodystrophy	BEFREE	2066109		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	8294459		★☆☆☆☆ Found in Text Mining only
Nephronophthisis	Nephronophthisis	BEFREE	24882706		★☆☆☆☆ Found in Text Mining only
Nephronophthisis familial juvenile	Nephronophthisis	Pubtator	24882706	Associate	★☆☆☆☆ Found in Text Mining only
Orofacial Cleft 1	Orofacial cleft	Pubtator	40147726	Associate	★☆☆☆☆ Found in Text Mining only
Orofaciodigital syndrome 9	Orofaciodigital syndrome	Pubtator	32253632, 37246745	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital Syndrome I	Orofaciodigital Syndrome	BEFREE	28486600		★☆☆☆☆ Found in Text Mining only
Orofaciodigital Syndromes	Orofaciodigital syndrome	GENOMICS_ENGLAND_DG	24285566		★☆☆☆☆ Found in Text Mining only
Orofaciodigital Syndromes	Orofaciodigital syndrome	BEFREE	24882706, 28486600		★☆☆☆☆ Found in Text Mining only
Orofaciodigital Syndromes	Orofaciodigital syndrome	Pubtator	24882706	Associate	★☆☆☆☆ Found in Text Mining only
Osteofibrous Dysplasia	Osteofibrous Dysplasia	BEFREE	28486600		★☆☆☆☆ Found in Text Mining only
Renal dysplasia and retinal aplasia (disorder)	Renal dysplasia and retinal aplasia	GENOMICS_ENGLAND_DG	24285566, 28005958, 30425282		★☆☆☆☆ Found in Text Mining only
Renal dysplasia and retinal aplasia (disorder)	Renal dysplasia and retinal aplasia	BEFREE	30425282		★☆☆☆☆ Found in Text Mining only
Retinal Degeneration	Retinal degeneration	Pubtator	37246745	Associate	★☆☆☆☆ Found in Text Mining only
Senior Loken Syndrome	Senior-loken syndrome	Pubtator	32253632, 37246745	Associate	★☆☆☆☆ Found in Text Mining only
Sjogren-Larsson Syndrome	Sjogren-Larsson Syndrome	BEFREE	30425282		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	8294459		★☆☆☆☆ Found in Text Mining only