SCLT1

sodium channel and clathrin linker 1

Basic information

Region (hg38): 4:128864921-129093600

Links

ENSG00000151466 ∙ NCBI:132320 ∙ OMIM:611399 ∙ HGNC:26406 ∙ Uniprot:Q96NL6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Senior-Loken syndrome (Limited), mode of inheritance: AR
• ciliopathy (Strong), mode of inheritance: AR
• retinitis pigmentosa (Limited), mode of inheritance: AR
• Bardet-Biedl syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCLT1 gene.

• not_provided (483 variants)
• not_specified (91 variants)
• SCLT1-related_disorder (64 variants)
• Retinal_dystrophy (17 variants)
• Congenital_hypothalamic_hamartoma_syndrome (2 variants)
• Esophageal_atresia/tracheoesophageal_fistula (2 variants)
• Opsoclonus (2 variants)
• Global_developmental_delay (2 variants)
• Hypermetropia (2 variants)
• Nystagmus (2 variants)
• Astigmatism (2 variants)
• Cone-rod_dystrophy (1 variants)
• Optic_atrophy (1 variants)
• Orofaciodigital_syndrome_IX (1 variants)
• Bardet-Biedl_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCLT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000144643.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	105	8	115
missense		1	219	12	5	237
nonsense	17		1			18
start loss						0
frameshift	16	3	1			20
splice donor/acceptor (+/-2bp)	1	15	1			17
Total	34	19	224	117	13

Highest pathogenic variant AF is 0.00009854769

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCLT1	protein_coding	protein_coding	ENST00000281142	21	228689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.269	341	327	1.04	0.0000160	4540
Missense in Polyphen		82	88.848	0.92293		1394
Synonymous	-0.715	120	110	1.09	0.00000509	1170
Loss of Function	2.18	32	48.4	0.661	0.00000243	594

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000867	0.000827
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.000222	0.000217
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000325	0.000316
Middle Eastern	0.000222	0.000217
South Asian	0.000275	0.000261
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein that links SCN10A to clathrin. Regulates SCN10A channel activity, possibly by promoting channel internalization (By similarity). {ECO:0000250}.
• Pathway: Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.0987

Intolerance Scores

• loftool: 0.970
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.84

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.863

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: clustering of voltage-gated sodium channels;cilium assembly;ciliary basal body-plasma membrane docking
• Cellular component: centrosome;centriole;cytosol;clathrin complex;ciliary transition fiber
• Molecular function: protein C-terminus binding;sodium channel regulator activity;clathrin binding