SEPTIN6

septin 6, the group of MicroRNA protein coding host genes|Septins

Basic information

Region (hg38): X:119615724-119693370

Previous symbols: [ "SEPT6" ]

Links

ENSG00000125354 ∙ NCBI:23157 ∙ OMIM:300683 ∙ HGNC:15848 ∙ Uniprot:Q14141 ∙ 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 SEPTIN6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN6 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				2		2
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	4	0

Variants in SEPTIN6

This is a list of pathogenic ClinVar variants found in the SEPTIN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-119629396-G-A		not specified	Uncertain significance (Jan 14, 2025)
X-119629415-C-T		not specified	Uncertain significance (Jan 19, 2025)
X-119629459-T-C		not specified	Uncertain significance (Dec 16, 2021)
X-119629489-C-T		not specified	Uncertain significance (Nov 07, 2022)
X-119633497-G-A		SEPTIN6-related disorder	Likely benign (Sep 23, 2020)
X-119637084-C-T		SEPTIN6-related disorder	Uncertain significance (Aug 22, 2024)
X-119637106-G-A		not specified	Uncertain significance (Sep 02, 2024)
X-119637140-G-A			Likely benign (Apr 01, 2023)
X-119637145-G-C		not specified	Uncertain significance (Aug 05, 2024)
X-119637159-C-T			Likely benign (Mar 01, 2023)
X-119640697-A-C		not specified	Uncertain significance (May 28, 2024)
X-119640710-G-T		not specified	Uncertain significance (Aug 21, 2023)
X-119640729-C-T		not specified	Uncertain significance (Sep 17, 2021)
X-119649942-T-C		not specified	Uncertain significance (Mar 08, 2025)
X-119650080-T-C		not specified	Uncertain significance (Jan 29, 2025)
X-119652870-T-G		not specified	Uncertain significance (Dec 08, 2023)
X-119652888-A-G		not specified	Uncertain significance (Feb 13, 2025)
X-119652962-T-G			Likely benign (May 01, 2022)
X-119653028-G-A		SEPTIN6-related disorder	Likely benign (Apr 20, 2023)
X-119663525-C-T		not specified	Uncertain significance (Aug 05, 2024)
X-119663551-C-T		not specified	Uncertain significance (Feb 26, 2025)
X-119663552-T-A		not specified	Uncertain significance (Mar 31, 2024)
X-119663567-A-C		not specified	Uncertain significance (Feb 25, 2025)
X-119663575-G-A		not specified	Uncertain significance (Oct 26, 2022)
X-119663636-A-G			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN6	protein_coding	protein_coding	ENST00000343984	10	77647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.932	0.0682	125619	0	3	125622	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	112	175	0.639	0.0000144	2884
Missense in Polyphen		50	93.69	0.53367		1537
Synonymous	0.402	70	74.4	0.941	0.00000666	793
Loss of Function	3.42	2	17.4	0.115	0.00000146	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000372	0.0000264
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. Required for normal organization of the actin cytoskeleton. Involved in cytokinesis. May play a role in HCV RNA replication. 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). {ECO:0000269|PubMed:17229681, ECO:0000269|PubMed:17803907, ECO:0000305|PubMed:25588830}.
• Pathway: Bacterial invasion of epithelial cells - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.111
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.461
• hipred: Y
• hipred_score: 0.749
• ghis: 0.652

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.358

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept6
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: sept6
• Affected structure: pronephric tubule
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Biological process: mitotic cytokinesis;spermatogenesis;viral process;cell differentiation;cilium assembly;cytoskeleton-dependent cytokinesis
• Cellular component: condensed chromosome kinetochore;spindle;septin ring;synaptic vesicle;microtubule cytoskeleton;midbody;septin complex;cleavage furrow;septin collar;axon terminus;sperm annulus
• Molecular function: GTPase activity;protein binding;GTP binding;protein-containing complex scaffold activity