SEPTIN10

septin 10, the group of Septins

Basic information

Region (hg38): 2:109542799-109614143

Previous symbols: [ "SEPT10" ]

Links

ENSG00000186522 ∙ NCBI:151011 ∙ OMIM:611737 ∙ HGNC:14349 ∙ Uniprot:Q9P0V9 ∙ 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 SEPTIN10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN10 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			47	1		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	47	1	0

Variants in SEPTIN10

This is a list of pathogenic ClinVar variants found in the SEPTIN10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-109546056-C-A		not specified	Uncertain significance (Apr 30, 2024)
2-109546224-A-G		not specified	Uncertain significance (Apr 07, 2022)
2-109546230-G-A		not specified	Uncertain significance (Sep 20, 2023)
2-109553172-C-A		not specified	Uncertain significance (May 18, 2022)
2-109553178-C-T		not specified	Uncertain significance (Nov 29, 2021)
2-109564462-C-A		not specified	Uncertain significance (Dec 17, 2023)
2-109564478-T-A		not specified	Uncertain significance (Jan 30, 2024)
2-109564489-A-G		not specified	Uncertain significance (Jan 23, 2024)
2-109564498-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-109565785-C-G		not specified	Uncertain significance (Jul 25, 2023)
2-109565787-G-C		not specified	Uncertain significance (Apr 07, 2022)
2-109565789-C-T		not specified	Uncertain significance (Nov 06, 2023)
2-109565790-G-A		not specified	Uncertain significance (Feb 10, 2022)
2-109565798-A-C		not specified	Uncertain significance (May 25, 2022)
2-109565799-C-T		not specified	Uncertain significance (Jun 07, 2023)
2-109565800-C-A		not specified	Uncertain significance (May 04, 2022)
2-109565803-C-G		not specified	Uncertain significance (Feb 15, 2023)
2-109565811-C-T		not specified	Uncertain significance (Oct 29, 2021)
2-109565829-T-C		not specified	Uncertain significance (Feb 28, 2023)
2-109565837-A-G		not specified	Uncertain significance (Oct 27, 2022)
2-109565845-A-C		not specified	Uncertain significance (Jun 18, 2021)
2-109565847-A-G		not specified	Uncertain significance (Sep 12, 2023)
2-109567846-T-C		not specified	Uncertain significance (Oct 12, 2021)
2-109567882-T-C		not specified	Uncertain significance (Aug 31, 2022)
2-109567910-T-C		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN10	protein_coding	protein_coding	ENST00000397712	11	71225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.74e-10	0.364	124719	0	76	124795	0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.14	285	236	1.21	0.0000123	3032
Missense in Polyphen		150	98.749	1.519		1244
Synonymous	1.06	68	80.1	0.849	0.00000419	782
Loss of Function	0.953	17	21.8	0.780	0.00000109	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000823	0.000818
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.0000556	0.0000556
Finnish	0.0000485	0.0000464
European (Non-Finnish)	0.000370	0.000362
Middle Eastern	0.0000556	0.0000556
South Asian	0.000230	0.000229
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Filament-forming cytoskeletal GTPase. May play a role in cytokinesis (Potential). {ECO:0000305}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.698
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.42

Haploinsufficiency Scores

• pHI: 0.508
• hipred: N
• hipred_score: 0.321
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.169

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept10
• 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); reproductive system phenotype; skeleton phenotype

Gene ontology

• Biological process: cytoskeleton-dependent cytokinesis
• Cellular component: septin ring;microtubule cytoskeleton;septin complex
• Molecular function: GTPase activity;protein binding;GTP binding;protein-containing complex scaffold activity