SEPTIN11

septin 11, the group of Septins

Basic information

Region (hg38): 4:76949751-77040384

Previous symbols: [ "SEPT11" ]

Links

ENSG00000138758 ∙ NCBI:55752 ∙ OMIM:612887 ∙ HGNC:25589 ∙ Uniprot:Q9NVA2 ∙ 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 SEPTIN11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN11 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			16			16
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in SEPTIN11

This is a list of pathogenic ClinVar variants found in the SEPTIN11 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-76949907-G-C		not specified	Uncertain significance (Aug 05, 2024)
4-76949923-G-A		not specified	Uncertain significance (Dec 19, 2022)
4-76996423-A-G			Uncertain significance (Aug 01, 2023)
4-77005676-A-G		not specified	Uncertain significance (Jun 05, 2023)
4-77005679-A-C		not specified	Uncertain significance (Apr 20, 2024)
4-77005694-G-A		not specified	Uncertain significance (Dec 20, 2023)
4-77005721-A-AG		Autosomal recessive cerebellar ataxia	Uncertain significance (Dec 01, 2020)
4-77005751-T-C		not specified	Uncertain significance (Oct 26, 2022)
4-77005782-A-G		not specified	Uncertain significance (May 04, 2022)
4-77011748-G-A		not specified	Uncertain significance (Mar 21, 2024)
4-77014968-A-C		not specified	Uncertain significance (Mar 12, 2024)
4-77014994-G-T		not specified	Uncertain significance (May 16, 2024)
4-77015006-G-A		not specified	Uncertain significance (Jul 07, 2024)
4-77019165-G-A		not specified	Uncertain significance (Dec 14, 2023)
4-77019196-C-G		not specified	Uncertain significance (Dec 13, 2023)
4-77019214-G-A		not specified	Uncertain significance (Jan 26, 2023)
4-77019224-G-C		not specified	Uncertain significance (Feb 15, 2023)
4-77020502-T-C		not specified	Uncertain significance (Jul 26, 2022)
4-77020538-G-A		not specified	Uncertain significance (Nov 07, 2024)
4-77020651-C-T		not specified	Uncertain significance (Aug 04, 2023)
4-77020668-C-G		not specified	Uncertain significance (Sep 21, 2021)
4-77030847-A-C		not specified	Uncertain significance (Oct 26, 2021)
4-77030895-C-T		not specified	Uncertain significance (Apr 12, 2022)
4-77030950-G-T		not specified	Uncertain significance (May 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN11	protein_coding	protein_coding	ENST00000264893	10	90682

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.959	0.0408	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	150	235	0.638	0.0000124	2881
Missense in Polyphen		42	96.865	0.43359		1174
Synonymous	1.25	72	86.8	0.830	0.00000478	751
Loss of Function	3.89	3	23.2	0.129	0.00000128	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000125
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000886	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Filament-forming cytoskeletal GTPase. May play a role in cytokinesis (Potential). May play a role in the cytoarchitecture of neurons, including dendritic arborization and dendritic spines, and in GABAergic synaptic connectivity (By similarity). During Listeria monocytogenes infection, not required for the bacterial entry process, but restricts its efficacy. {ECO:0000250, ECO:0000269|PubMed:15196925, ECO:0000269|PubMed:19234302, ECO:0000305}.
• Pathway: Bacterial invasion of epithelial cells - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.332
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.572
• ghis: 0.688

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept11

Gene ontology

• Biological process: regulation of synapse organization;protein heterooligomerization;cytoskeleton-dependent cytokinesis
• Cellular component: stress fiber;septin ring;microtubule cytoskeleton;cell junction;axon;septin complex;dendritic spine;glutamatergic synapse;GABA-ergic synapse;postsynaptic specialization of symmetric synapse
• Molecular function: GTPase activity;protein binding;GTP binding;protein-containing complex scaffold activity