SEPTIN9 septin 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SEPTIN9provided by HGNC
Official Full Name: septin 9provided by HGNC
Primary source: HGNC:HGNC:7323
See related: Ensembl:ENSG00000184640 MIM:604061; AllianceGenome:HGNC:7323
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MSF; MSF1; NAPB; SEPT9; SINT1; PNUTL4; SeptD1; AF17q25
Summary: This gene is a member of the septin family involved in cytokinesis and cell cycle control. This gene is a candidate for the ovarian tumor suppressor gene. Mutations in this gene cause hereditary neuralgic amyotrophy, also known as neuritis with brachial predilection. A chromosomal translocation involving this gene on chromosome 17 and the MLL gene on chromosome 11 results in acute myelomonocytic leukemia. Multiple alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Mar 2009]
Expression: Ubiquitous expression in spleen (RPKM 19.8), lymph node (RPKM 19.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q25.3

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (77281499..77500596)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (78174746..78394627)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (75277581..75496678)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SEPT9: From pan-cancer to lung squamous cell carcinoma.
Title: SEPT9: From pan-cancer to lung squamous cell carcinoma.
Diagnostic efficacy of SEPT9 and PAX5 gene methylation in gastrointestinal cancer and precancerous lesions.
Title: Diagnostic efficacy of SEPT9 and PAX5 gene methylation in gastrointestinal cancer and precancerous lesions.
Association of Methylenetetrahydrofolate Reductase rs1801133 Gene Polymorphism with Cancer Risk and Septin 9 Methylation in Patients with Colorectal Cancer.
Title: Association of Methylenetetrahydrofolate Reductase rs1801133 Gene Polymorphism with Cancer Risk and Septin 9 Methylation in Patients with Colorectal Cancer.
The concerted action of SEPT9 and EPLIN modulates the adhesion and migration of human fibroblasts.
Title: The concerted action of SEPT9 and EPLIN modulates the adhesion and migration of human fibroblasts.
Septin9 DNA methylation is associated with breast cancer recurrence or metastasis.
Title: Septin9 DNA methylation is associated with breast cancer recurrence or metastasis.
SEPT9, H4C6, and RASSF1A methylation in nasopharyngeal swabs: A reflection of potential minimally invasive biomarkers for early screening of nasopharyngeal cancer.
Title: SEPT9, H4C6, and RASSF1A methylation in nasopharyngeal swabs: A reflection of potential minimally invasive biomarkers for early screening of nasopharyngeal cancer.
Circulating Cell-Free SEPT9 DNA Methylation in Blood Is a Biomarker for Minimal Residual Disease Detection in Head and Neck Squamous Cell Carcinoma Patients.
Title: Circulating Cell-Free SEPT9 DNA Methylation in Blood Is a Biomarker for Minimal Residual Disease Detection in Head and Neck Squamous Cell Carcinoma Patients.
Septin 9 Orients the Apico-Basal Polarity Axis and Controls Plasticity Signals.
Title: Septin 9 Orients the Apico-Basal Polarity Axis and Controls Plasticity Signals.
Analyzing the Role of Septin9 Gene Methylation in the Diagnosis and Treatment of Primary Liver Cancer in the Elderly.
Title: Analyzing the Role of Septin9 Gene Methylation in the Diagnosis and Treatment of Primary Liver Cancer in the Elderly.
SEPT9 Expression in Hepatic Nodules: An Immunohistochemical Study of Hepatocellular Neoplasm and Metastasis.
Title: SEPT9 Expression in Hepatic Nodules: An Immunohistochemical Study of Hepatocellular Neoplasm and Metastasis.

Submit: New GeneRIF Correction See all GeneRIFs (112)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Amyotrophic neuralgia MedGen: C1834304 OMIM: 162100 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study of behavioral disinhibition. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	FITC-labeled Tat 47-59 peptide upregulates gene expression of septin 9 (SEPT9) in U-937 macrophages	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH98696 (e-PCR)
- UniSTS:91416

RH121931 (e-PCR)
- UniSTS:95004

D17S1603 (e-PCR), detects polymorphism
- UniSTS:50771

D17S705 (e-PCR)
- UniSTS:35180

D17S937 (e-PCR), detects polymorphism
- UniSTS:28301

SHGC-111980 (e-PCR)
- UniSTS:168848

RH98887 (e-PCR)
- UniSTS:91039

D17S939 (e-PCR)
- UniSTS:13733

AFM267xh1 (e-PCR), detects polymorphism
- UniSTS:85191

RH45518 (e-PCR)
- UniSTS:19151

D17S802 (e-PCR), detects polymorphism
- UniSTS:48363

SHGC-112100 (e-PCR)
- UniSTS:183023

RH35918 (e-PCR)
- UniSTS:16123

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cadherin binding	HDA more info	PubMed
enables molecular adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cytoskeleton-dependent cytokinesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of non-motile cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info
located_in axoneme	IDA Inferred from Direct Assay more info	PubMed
is_active_in cell division site	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in microtubule	IDA Inferred from Direct Assay more info	PubMed
is_active_in microtubule cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
located_in non-motile cilium	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of septin complex	IBA Inferred from Biological aspect of Ancestor more info
part_of septin complex	IDA Inferred from Direct Assay more info	PubMed
part_of septin complex	ISS Inferred from Sequence or Structural Similarity more info
is_active_in septin ring	IBA Inferred from Biological aspect of Ancestor more info
located_in stress fiber	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: septin-9

Names: MLL septin-like fusion protein MSF-A; Ov/Br septin; ovarian/breast septin; peanut-like 4; septin D1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_011683.2 RefSeqGene

Range

5090..224184

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_370

mRNA and Protein(s)

NM_001113491.2 → NP_001106963.1 septin-9 isoform a

See identical proteins and their annotated locations for NP_001106963.1

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as epsilon) encodes the longest isoform (a).

Source sequence(s)

AC068594, AC111170, AC111182

Consensus CDS

CCDS45790.1

UniProtKB/Swiss-Prot

A8K2V3, B3KPM0, B4DTL9, B4E0N2, B4E274, B7Z654, Q96QF3, Q96QF4, Q96QF5, Q9HA04, Q9UG40, Q9UHD8, Q9Y5W4

Related

ENSP00000391249.1, ENST00000427177.6

Conserved Domains (2) summary

cd01850
Location:295 → 569

CDC_Septin; CDC/Septin GTPase family

COG5019
Location:277 → 583

CDC3; Septin family protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
NM_001113492.2 → NP_001106964.1 septin-9 isoform e

See identical proteins and their annotated locations for NP_001106964.1

Status: REVIEWED

Description

Transcript Variant: This variant (5, also known as zeta or v4*) lacks the first 5' exon, but has an alternate 5' exon, which results in a downstream AUG start codon, as compared to variant 1. The resulting isoform (e) has a shorter N-terminus, as compared to isoform a.

Source sequence(s)

AC068594, AC111170, AC111182

Consensus CDS

CCDS45793.1

UniProtKB/TrEMBL

A0A0S2Z5W9

Related

ENSP00000400181.2, ENST00000449803.6

Conserved Domains (2) summary

cd01850
Location:131 → 405

CDC_Septin; CDC/Septin GTPase family

COG5019
Location:113 → 419

CDC3; Septin family protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
NM_001113493.2 → NP_001106965.1 septin-9 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as gamma) lacks two 5' exons but has an alternate 5' exon, as compared to variant 1. The resulting isoform (b) has a shorter and different N-terminus, as compared to isoform a.

Source sequence(s)

AC111170, AC111182

Consensus CDS

CCDS45792.1

Related

ENSP00000405877.1, ENST00000423034.6

Conserved Domains (2) summary

cd01850
Location:288 → 562

CDC_Septin; CDC/Septin GTPase family

COG5019
Location:270 → 576

CDC3; Septin family protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
NM_001113494.1 → NP_001106966.1 septin-9 isoform e

See identical proteins and their annotated locations for NP_001106966.1

Status: REVIEWED

Description

Transcript Variant: This variant (6, also known as beta or v4) lacks two 5' exons but has an alternate 5' exon, which results in a downstream AUG start codon, as compared to variant 1. The resulting isoform (e) has a shorter N-terminus,as compared to isoform a.

Source sequence(s)

AA523782, AB023208, BC064642, BQ279153, DA234895, DB007851

Consensus CDS

CCDS45793.1

UniProtKB/TrEMBL

A0A0S2Z5W9

Related

ENSP00000403194.1, ENST00000427674.6

Conserved Domains (2) summary

cd01850
Location:131 → 405

CDC_Septin; CDC/Septin GTPase family

COG5019
Location:113 → 419

CDC3; Septin family protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
NM_001113495.2 → NP_001106967.2 septin-9 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (4) encodes isoform f.

Source sequence(s)

AC111170

Consensus CDS

CCDS45795.1

UniProtKB/TrEMBL

A0A0S2Z5W9

Related

ENSP00000504196.1, ENST00000427180.5

Conserved Domains (1) summary

cd01850
Location:44 → 318

CDC_Septin; CDC/Septin GTPase family
NM_001113496.2 → NP_001106968.1 septin-9 isoform f

See identical proteins and their annotated locations for NP_001106968.1

Status: REVIEWED

Description

Transcript Variant: This variant (7, also known as delta) lacks three 5' exons, but has an alternate 5' exon, which results in a downstream AUG start codon, as compared to variant 1. The resulting isoform (f) has a much shorter N-terminus, as compared to isoform a.

Source sequence(s)

AC111170

Consensus CDS

CCDS45795.1

UniProtKB/TrEMBL

A0A0S2Z5W9

Related

ENSP00000438089.2, ENST00000541152.6

Conserved Domains (1) summary

cd01850
Location:44 → 318

CDC_Septin; CDC/Septin GTPase family
NM_001293695.2 → NP_001280624.1 septin-9 isoform g

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks an in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (g) lacks an internal segment, compared to isoform a.

Source sequence(s)

AC068594, AC111170, AC111182

Consensus CDS

CCDS77122.1

Related

ENSP00000468406.1, ENST00000591198.5

Conserved Domains (2) summary

cd01850
Location:276 → 550

CDC_Septin; CDC/Septin GTPase family

COG5019
Location:258 → 564

CDC3; Septin family protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
NM_001293696.2 → NP_001280625.1 septin-9 isoform h

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks three 5' exons, but has an alternate 5' exon, as compared to variant 1. The resulting isoform (h) has a distinct and shorter N-terminus, as compared to isoform a.

Source sequence(s)

AC111170, AC111182

Consensus CDS

CCDS74166.1

UniProtKB/TrEMBL

A0A0S2Z5W9

Related

ENSP00000468120.1, ENST00000585930.5

Conserved Domains (2) summary

cd01850
Location:71 → 345

CDC_Septin; CDC/Septin GTPase family

COG5019
Location:53 → 359

CDC3; Septin family protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
NM_001293697.2 → NP_001280626.1 septin-9 isoform f

See identical proteins and their annotated locations for NP_001280626.1

Status: REVIEWED

Description

Transcript Variant: This variant (10) lacks three 5' exons, but has an alternate 5' exon, which results in a downstream AUG start codon, as compared to variant 1. The resulting isoform (f) has a much shorter N-terminus, as compared to isoform a. Variants 7, 10 and 11 encode the same isoform f.

Source sequence(s)

AC111170

Consensus CDS

CCDS45795.1

UniProtKB/TrEMBL

A0A0S2Z5W9

Related

ENSP00000466247.1, ENST00000591088.5

Conserved Domains (1) summary

cd01850
Location:44 → 318

CDC_Septin; CDC/Septin GTPase family
NM_001293698.2 → NP_001280627.1 septin-9 isoform f

See identical proteins and their annotated locations for NP_001280627.1

Status: REVIEWED

Description

Transcript Variant: This variant (11) lacks three 5' exons, but has an alternate 5' exon, which results in a downstream AUG start codon, as compared to variant 1. The resulting isoform (f) has a much shorter N-terminus, as compared to isoform a.

Source sequence(s)

AC111170

Consensus CDS

CCDS45795.1

UniProtKB/TrEMBL

A0A0S2Z5W9

Related

ENSP00000466648.1, ENST00000592951.5

Conserved Domains (1) summary

cd01850
Location:44 → 318

CDC_Septin; CDC/Septin GTPase family
NM_006640.5 → NP_006631.2 septin-9 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3, also known as alpha) lacks two 5' exons but has an alternate 5' exon, as compared to variant 1. The resulting isoform (c) has a shorter and different N-terminus, as compared to isoform a.

Source sequence(s)

AC111170, AC111182

Consensus CDS

CCDS45791.1

UniProtKB/TrEMBL

A0A0S2Z5A5

Related

ENSP00000329161.8, ENST00000329047.13

Conserved Domains (2) summary

cd01850
Location:277 → 551

CDC_Septin; CDC/Septin GTPase family

COG5019
Location:259 → 565

CDC3; Septin family protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]