SEPTIN1

septin 1, the group of Septins

Basic information

Region (hg38): 16:30378135-30395991

Previous symbols: [ "DIFF6", "SEPT1" ]

Links

ENSG00000180096 ∙ NCBI:1731 ∙ OMIM:612897 ∙ HGNC:2879 ∙ Uniprot:Q8WYJ6 ∙ 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 SEPTIN1 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	2	0	0

Variants in SEPTIN1

This is a list of pathogenic ClinVar variants found in the SEPTIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30395814-C-G		not specified	Uncertain significance (May 17, 2023)
16-30395840-G-C		not specified	Uncertain significance (Jun 21, 2022)
16-30395843-G-A		not specified	Uncertain significance (Mar 16, 2024)
16-30395847-G-C		not specified	Uncertain significance (Oct 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN1	protein_coding	protein_coding	ENST00000321367	12	17859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.77e-8	0.890	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	180	250	0.721	0.0000142	2677
Missense in Polyphen		60	90.465	0.66324		949
Synonymous	0.158	93	95.0	0.979	0.00000529	786
Loss of Function	1.68	15	23.9	0.629	0.00000111	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000164	0.000163
South Asian	0.000362	0.000359
Other	0.000163	0.000163

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);Aurora B signaling (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.0704
• hipred: Y
• hipred_score: 0.639
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.451

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept1

Gene ontology

• Biological process: regulation of exocytosis;cytoskeleton-dependent cytokinesis
• Cellular component: microtubule organizing center;septin ring;synaptic vesicle;microtubule cytoskeleton;midbody;septin complex
• Molecular function: GTPase activity;protein binding;GTP binding;protein-containing complex scaffold activity;identical protein binding