GeneBe

SEPTIN6

protein-coding

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

Gene summary

This gene is a member of the septin family of GTPases. Members of this family are required for cytokinesis. One version of pediatric acute myeloid leukemia is the result of a reciprocal translocation between chromosomes 11 and X, with the breakpoint associated with the genes encoding the mixed-lineage leukemia and septin 2 proteins. This gene encodes four transcript variants encoding three distinct isoforms. An additional transcript variant has been identified, but its biological validity has not been determined. [provided by RefSeq, Jul 2008]

Previous symbols:
  • SEPT6

MANE transcript

NM_145799.4

Inheritance

—

ClinVar variants

U:112B:6

Top phenotype

SEPTIN6-related disorder

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chrX:119,615,724-119,693,370

External References & Databases

Ensembl (ENSG00000125354)NCBI Gene (23157)OMIM (300683)HGNC:15848GenCCUniProt (Q14141)AlphaFoldClinVar (SEPTIN6)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~77.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SEPTIN6 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 28
SEPTIN6-related disorderTotal: 8
not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145799.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
9
clinvar
4
clinvar
 13
missense
67
clinvar
2
clinvar
 69
nonsense
8
clinvar
 8
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
28
clinvar
 28
Total0011260118
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_145799.4RefSeqNP_665798.110MANE Select
ENST00000394610.7EnsemblENSP00000378108.110MANE Select
NM_001410710.1RefSeqNP_001397639.110Standard
NM_015129.6RefSeqNP_055944.210Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
sept6Danio rerio

Structure: pronephric tubule

Quality: dilated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Bacterial invasion of epithelial cells - Homo sapiens (human)

Biological Process

  • mitotic cytokinesis
  • spermatogenesis
  • viral process
  • cell differentiation
  • cilium assembly

Molecular Function

  • GTPase activity
  • protein binding
  • GTP binding
  • protein-containing complex scaffold activity

Cellular Component

  • condensed chromosome kinetochore
  • spindle
  • septin ring
  • synaptic vesicle
  • microtubule cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000343984
Coding exons
10
Length
77647
Individuals with no LoFs
125619
Homozygous LoFs
0
Heterozygous LoFs
3
Defined
125622
p
0.0000119
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.701121750.6390.00001442884
Missense (PolyPhen)5093.690.533671537
Synonymous0.4027074.40.9410.00000666793
Loss of Function3.42217.40.1150.00000146266

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000370.000026rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.146

Intolerance Scores

LoFtool
0.111
RVIS EVS
-0.25
RVIS percentile EVS
35.42

Essentials

Essential (CRISPR)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.358

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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