SNTN

sentan, cilia apical structure protein

Basic information

Region (hg38): 3:63652675-63679020

Links

ENSG00000188817 ∙ NCBI:132203 ∙ OMIM:617832 ∙ HGNC:33706 ∙ Uniprot:A6NMZ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNTN 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						0
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in SNTN

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

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

Position	Type	Phenotype	Significance	ClinVar
3-63652703-C-A		not specified	Uncertain significance (Jan 29, 2025)
3-63652739-G-A		not specified	Uncertain significance (Jun 17, 2024)
3-63652746-A-G		not specified	Uncertain significance (Oct 06, 2021)
3-63652775-G-A		not specified	Uncertain significance (Aug 17, 2021)
3-63659736-T-C		not specified	Uncertain significance (Dec 01, 2022)
3-63659748-G-C		not specified	Uncertain significance (Mar 29, 2022)
3-63659785-A-T		not specified	Uncertain significance (Aug 27, 2024)
3-63663967-A-T		not specified	Uncertain significance (Dec 22, 2023)
3-63664072-C-T		not specified	Likely benign (Jan 17, 2023)
3-63664073-G-A		not specified	Uncertain significance (Oct 12, 2021)
3-63664083-A-C		not specified	Uncertain significance (Dec 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNTN	protein_coding	protein_coding	ENST00000343837	4	26353

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000103	0.372	125710	0	31	125741	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.132	72	75.2	0.957	0.00000350	966
Missense in Polyphen		19	17.491	1.0863		276
Synonymous	-0.488	29	25.8	1.12	0.00000119	278
Loss of Function	0.0352	6	6.09	0.985	2.55e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a component of the linker structure that bridges the ciliary membrane and peripheral singlet microtubules. {ECO:0000250}.

Intolerance Scores

• loftool: 0.714
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.171
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sntn

Gene ontology

• Cellular component: cilium
• Molecular function: transition metal ion binding