SCLT1

sodium channel and clathrin linker 1

Basic information

Region (hg38): 4:128864920-129093600

Links

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

Phenotypes

GenCC

Source: genCC

• Bardet-Biedl syndrome (Limited), mode of inheritance: AR
• Senior-Loken 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 (398 variants)
• Inborn genetic diseases (39 variants)
• 6 conditions (2 variants)
• Tracheoesophageal fistula (2 variants)
• SCLT1-related disorder (2 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				69	10	79
missense			177	2	8	187
nonsense	9					9
start loss						0
frameshift	13	1				14
inframe indel			3			3
splice donor/acceptor (+/-2bp)	1	9				10
splice region			9	11	3	23
non coding	1		20	61	12	94
Total	24	10	200	132	30

Highest pathogenic variant AF is 0.0000657

Variants in SCLT1

This is a list of pathogenic ClinVar variants found in the SCLT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-128867901-C-T		not specified	Uncertain significance (Feb 28, 2023)
4-128871384-C-A		not specified	Uncertain significance (Feb 28, 2023)
4-128871517-A-G		not specified	Uncertain significance (Aug 09, 2021)
4-128871522-C-G		not specified	Uncertain significance (Jun 24, 2022)
4-128871523-G-A		not specified	Uncertain significance (Oct 10, 2023)
4-128871632-A-G			Benign (Jun 27, 2018)
4-128871702-G-A		not specified	Uncertain significance (Jan 04, 2022)
4-128871718-A-G			Benign (Jun 27, 2018)
4-128871735-C-T		not specified	Uncertain significance (Apr 07, 2023)
4-128871783-C-T		not specified	Uncertain significance (Jul 13, 2022)
4-128871784-C-T		not specified	Uncertain significance (Oct 02, 2023)
4-128871808-A-G		not specified	Uncertain significance (May 31, 2023)
4-128871847-G-C		not specified	Uncertain significance (Nov 02, 2023)
4-128871978-G-A		not specified	Uncertain significance (Aug 30, 2021)
4-128871987-C-T		not specified	Uncertain significance (Oct 13, 2023)
4-128872032-G-C		not specified	Uncertain significance (Mar 31, 2022)
4-128872065-T-C		not specified	Uncertain significance (Dec 20, 2021)
4-128872081-G-A		not specified	Uncertain significance (Sep 17, 2021)
4-128872087-C-T		not specified	Uncertain significance (Jan 26, 2023)
4-128872212-A-G		not specified	Uncertain significance (Dec 05, 2022)
4-128884478-T-A			Uncertain significance (Aug 27, 2021)
4-128884479-A-G			Likely benign (Jan 10, 2024)
4-128884483-A-AT		6 conditions	Likely pathogenic (Aug 28, 2020)
4-128884498-C-A			Likely benign (Feb 03, 2022)
4-128884518-T-G			Likely benign (Jan 18, 2024)

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
4.38e-16	0.897	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

Haploinsufficiency Scores

• pHI: 0.345
• hipred: N
• hipred_score: 0.253
• ghis: 0.576

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

Mouse Genome Informatics

• Gene name: Sclt1
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); limbs/digits/tail phenotype; digestive/alimentary phenotype; renal/urinary system phenotype

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