SEPTIN3

septin 3, the group of Septins

Basic information

Region (hg38): 22:41969442-41998221

Previous symbols: [ "SEP3", "SEPT3" ]

Links

ENSG00000100167 ∙ NCBI:55964 ∙ OMIM:608314 ∙ HGNC:10750 ∙ Uniprot:Q9UH03 ∙ 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 SEPTIN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN3 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			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in SEPTIN3

This is a list of pathogenic ClinVar variants found in the SEPTIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-41981711-C-T			Benign (Apr 02, 2018)
22-41981800-A-G		not specified	Uncertain significance (Jan 16, 2024)
22-41986043-C-T		not specified	Uncertain significance (Nov 08, 2022)
22-41986065-G-A		not specified	Uncertain significance (Jan 09, 2024)
22-41987241-G-A		not specified	Uncertain significance (Jul 07, 2022)
22-41987267-C-G		not specified	Uncertain significance (Oct 26, 2023)
22-41987645-T-C		not specified	Uncertain significance (May 16, 2022)
22-41987702-G-A		not specified	Uncertain significance (Jun 26, 2023)
22-41989610-G-A		not specified	Uncertain significance (Mar 02, 2023)
22-41989680-A-G		not specified	Uncertain significance (Sep 14, 2023)
22-41992723-G-C		not specified	Uncertain significance (Apr 19, 2023)
22-41994713-C-T		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN3	protein_coding	protein_coding	ENST00000396426	11	21950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0894	0.910	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	113	215	0.525	0.0000122	2381
Missense in Polyphen		38	90.724	0.41885		1034
Synonymous	0.0796	80	80.9	0.989	0.00000486	656
Loss of Function	3.14	6	21.8	0.275	0.00000125	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00130	0.00129
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Filament-forming cytoskeletal GTPase (By similarity). May play a role in cytokinesis (Potential). {ECO:0000250, ECO:0000305}.
• Pathway: Bacterial invasion of epithelial cells - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.608
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.292
• hipred: Y
• hipred_score: 0.802
• ghis: 0.659

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.381

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept3
• Phenotype: 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); normal phenotype

Gene ontology

• Biological process: cytoskeleton-dependent cytokinesis
• Cellular component: septin ring;microtubule cytoskeleton;cell junction;septin complex;neuron projection;presynaptic cytoskeleton
• Molecular function: molecular_function;GTPase activity;protein binding;GTP binding;protein-containing complex scaffold activity;identical protein binding