SEPTIN5

septin 5, the group of Septins

Basic information

Region (hg38): 22:19714503-19724224

Previous symbols: [ "PNUTL1", "SEPT5" ]

Links

ENSG00000184702 ∙ NCBI:5413 ∙ OMIM:602724 ∙ HGNC:9164 ∙ Uniprot:Q99719 ∙ 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 SEPTIN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN5 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				5	1	6
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				2		2
Total	0	0	18	8	1

Variants in SEPTIN5

This is a list of pathogenic ClinVar variants found in the SEPTIN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-19714616-A-C		not specified	Uncertain significance (Aug 02, 2023)
22-19714623-C-T		not specified	Uncertain significance (May 31, 2022)
22-19714624-G-A			Benign (Sep 12, 2018)
22-19719689-A-G		not specified	Uncertain significance (Oct 20, 2024)
22-19719838-C-A		not specified	Uncertain significance (Oct 03, 2022)
22-19719867-G-T		not specified	Uncertain significance (Aug 02, 2023)
22-19719871-C-T		not specified	Uncertain significance (Nov 14, 2024)
22-19719872-G-A		not specified	Uncertain significance (Dec 06, 2024)
22-19719874-A-C		not specified	Uncertain significance (Jan 22, 2024)
22-19720124-G-A		not specified	Likely benign (May 26, 2023)
22-19720141-C-G		not specified	Uncertain significance (Dec 02, 2021)
22-19720192-A-G		not specified	Uncertain significance (Dec 27, 2023)
22-19720202-C-T		not specified	Uncertain significance (Jan 16, 2024)
22-19720336-G-A		not specified	Uncertain significance (Jul 27, 2024)
22-19720346-A-C		not specified	Uncertain significance (Sep 16, 2021)
22-19720369-C-T		not specified	Uncertain significance (Oct 26, 2024)
22-19720388-A-T		not specified	Uncertain significance (Sep 10, 2024)
22-19720439-C-G		not specified	Uncertain significance (Jan 03, 2024)
22-19720446-C-G		not specified	Uncertain significance (Jan 10, 2022)
22-19720550-C-T			Likely benign (Jul 16, 2018)
22-19720553-C-T		not specified	Uncertain significance (Mar 28, 2023)
22-19720675-G-A			Likely benign (Apr 03, 2018)
22-19720772-G-A		not specified	Uncertain significance (Feb 28, 2024)
22-19720845-C-T			Likely benign (May 21, 2018)
22-19720858-C-T		not specified	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN5	protein_coding	protein_coding	ENST00000455784	12	10309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.927	0.0733	125521	0	7	125528	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	128	243	0.526	0.0000157	2459
Missense in Polyphen		58	120.16	0.48268		1137
Synonymous	-0.749	111	101	1.09	0.00000727	664
Loss of Function	3.70	3	21.6	0.139	0.00000106	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Filament-forming cytoskeletal GTPase (By similarity). May play a role in cytokinesis (Potential). May play a role in platelet secretion (By similarity). {ECO:0000250, ECO:0000305}.
• Pathway: Parkinson,s disease - Homo sapiens (human);Parkin-Ubiquitin Proteasomal System pathway;Parkinsons Disease Pathway (Consensus)

Recessive Scores

• pRec: 0.278

Intolerance Scores

• loftool: 0.413
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.882
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept5
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: synaptic vesicle targeting;regulation of exocytosis;cytoskeleton-dependent cytokinesis;regulation of synaptic vesicle exocytosis
• Cellular component: plasma membrane;septin ring;synaptic vesicle;microtubule cytoskeleton;septin complex
• Molecular function: GTPase activity;structural molecule activity;protein binding;GTP binding;protein-containing complex scaffold activity