SEPTIN2

septin 2, the group of Septins

Basic information

Region (hg38): 2:241315099-241354027

Previous symbols: [ "DIFF6", "NEDD5", "SEPT2" ]

Links

ENSG00000168385 ∙ NCBI:4735 ∙ OMIM:601506 ∙ HGNC:7729 ∙ Uniprot:Q15019 ∙ 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 SEPTIN2 gene.

• Inborn genetic diseases (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN2 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					1	1
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	1

Variants in SEPTIN2

This is a list of pathogenic ClinVar variants found in the SEPTIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-241326003-C-A		not specified	Uncertain significance (May 30, 2023)
2-241335147-C-T		not specified	Uncertain significance (Feb 28, 2023)
2-241335178-T-A		not specified	Uncertain significance (Apr 11, 2023)
2-241336010-A-G		not specified	Uncertain significance (Jul 20, 2022)
2-241337513-A-G		not specified	Uncertain significance (Jul 17, 2023)
2-241337694-G-A			Benign (Aug 28, 2018)
2-241343077-A-C		not specified	Uncertain significance (May 04, 2022)
2-241350136-G-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN2	protein_coding	protein_coding	ENST00000391973	11	38928

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.288	0.712	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	125	205	0.609	0.0000112	2394
Missense in Polyphen		35	91.912	0.3808		1107
Synonymous	-1.02	83	72.0	1.15	0.00000394	654
Loss of Function	3.26	5	21.2	0.236	0.00000107	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000339	0.000335
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Filament-forming cytoskeletal GTPase. Forms a filamentous structure with SEPT12, SEPT6, SEPT2 and probably SEPT4 at the sperm annulus which is required for the structural integrity and motility of the sperm tail during postmeiotic differentiation (PubMed:25588830). Required for normal organization of the actin cytoskeleton. Plays a role in the biogenesis of polarized columnar-shaped epithelium by maintaining polyglutamylated microtubules, thus facilitating efficient vesicle transport, and by impeding MAP4 binding to tubulin. Required for the progression through mitosis. Forms a scaffold at the midplane of the mitotic splindle required to maintain CENPE localization at kinetochores and consequently chromosome congression. During anaphase, may be required for chromosome segregation and spindle elongation. Plays a role in ciliogenesis and collective cell movements. In cilia, required for the integrity of the diffusion barrier at the base of the primary cilium that prevents diffusion of transmembrane proteins between the cilia and plasma membranes: probably acts by regulating the assembly of the tectonic-like complex (also named B9 complex) by localizing TMEM231 protein. May play a role in the internalization of 2 intracellular microbial pathogens, Listeria monocytogenes and Shigella flexneri. {ECO:0000269|PubMed:15774761, ECO:0000269|PubMed:17803907, ECO:0000269|PubMed:18209106, ECO:0000269|PubMed:19145258, ECO:0000305|PubMed:25588830}.
• Pathway: Bacterial invasion of epithelial cells - Homo sapiens (human);Anchoring of the basal body to the plasma membrane;CDC42 signaling events;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.752
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.220
• hipred: Y
• hipred_score: 0.696
• ghis: 0.652

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept2

Gene ontology

• Biological process: smoothened signaling pathway;spermatogenesis;neuron projection development;cilium assembly;cytoskeleton-dependent cytokinesis
• Cellular component: exocyst;condensed chromosome kinetochore;nucleus;cytoplasm;spindle;axoneme;cell cortex;septin ring;microtubule cytoskeleton;midbody;septin complex;cleavage furrow;photoreceptor connecting cilium;perinuclear region of cytoplasm;ciliary membrane;extracellular exosome;sperm annulus;non-motile cilium
• Molecular function: GTPase activity;protein binding;GTP binding;protein-containing complex scaffold activity;cadherin binding