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SEPTIN9 septin 9 [ Homo sapiens (human) ]

Gene ID: 10801, updated on 5-Mar-2023

Summary

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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
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Genomic context

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See SEPTIN9 in Genome Data Viewer
Location:
17q25.3
Exon count:
21
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (77281499..77500596)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (78174746..78394627)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (75277581..75496678)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 14112 Neighboring gene lung adenocarcinoma-associated transcript 1 Neighboring gene SEPTIN9 divergent transcript Neighboring gene HNF4 motif-containing MPRA enhancer 212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75359740-75360398 Neighboring gene uncharacterized LOC124904062 Neighboring gene uncharacterized LOC112268199 Neighboring gene microRNA 4316 Neighboring gene uncharacterized LOC112268198 Neighboring gene uncharacterized LOC105371903 Neighboring gene uncharacterized LOC400622 Neighboring gene uncharacterized LOC100507351 Neighboring gene uncharacterized LOC124904103

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Septin 9 methylation analysis of lymph node micrometastases for predicting relapse of colorectal cancer. Wan Y, et al. Ann Diagn Pathol, 2022 Oct. PMID 35939880
  2. Methylated Septin 9 as a Promising Biomarker in the Diagnosis and Recurrence Monitoring of Colorectal Cancer. Lu P, et al. Dis Markers, 2022. PMID 35818587, Free PMC Article
  3. Methylated Septin9 has moderate diagnostic value in colorectal cancer detection in Chinese population: a multicenter study. Lu DC, et al. BMC Gastroenterol, 2022 May 11. PMID 35546391, Free PMC Article
  4. Distinct Performance of Methylated SEPT9 in Upper and Lower Gastrointestinal Cancers and Combined Detection with Protein Markers. Tang H, et al. Genet Test Mol Biomarkers, 2022 Apr. PMID 35481971
  5. Application of droplet digital polymerase chain reaction of plasma methylated septin 9 on detection and early monitoring of colorectal cancer. Ma ZY, et al. Sci Rep, 2021 Dec 6. PMID 34873218, Free PMC Article

See all (235) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Septin 9 methylation analysis of lymph node micrometastases for predicting relapse of colorectal cancer.
    Title: Septin 9 methylation analysis of lymph node micrometastases for predicting relapse of colorectal cancer.
  2. Circular RNA circSEPT9 Is Upregulated in Endometrial Cancer and Promotes Cell Invasion and Migration by Downregulating miR-186 through Methylation.
    Title: Circular RNA circSEPT9 Is Upregulated in Endometrial Cancer and Promotes Cell Invasion and Migration by Downregulating miR-186 through Methylation.
  3. Methylated Septin 9 as a Promising Biomarker in the Diagnosis and Recurrence Monitoring of Colorectal Cancer.
    Title: Methylated Septin 9 as a Promising Biomarker in the Diagnosis and Recurrence Monitoring of Colorectal Cancer.
  4. Methylated Septin9 has moderate diagnostic value in colorectal cancer detection in Chinese population: a multicenter study.
    Title: Methylated Septin9 has moderate diagnostic value in colorectal cancer detection in Chinese population: a multicenter study.
  5. Distinct Performance of Methylated SEPT9 in Upper and Lower Gastrointestinal Cancers and Combined Detection with Protein Markers.
    Title: Distinct Performance of Methylated SEPT9 in Upper and Lower Gastrointestinal Cancers and Combined Detection with Protein Markers.
  6. ARHGAP4-SEPT2-SEPT9 complex enables both up- and down-modulation of integrin-mediated focal adhesions, cell migration, and invasion.
    Title: ARHGAP4-SEPT2-SEPT9 complex enables both up- and down-modulation of integrin-mediated focal adhesions, cell migration, and invasion.
  7. Noninvasive Detection of Esophageal Cancer by the Combination of mSEPT9 and SNCG.
    Title: Noninvasive Detection of Esophageal Cancer by the Combination of mSEPT9 and SNCG.
  8. Septin-microtubule association via a motif unique to isoform 1 of septin 9 tunes stress fibers.
    Title: Septin-microtubule association via a motif unique to isoform 1 of septin 9 tunes stress fibers.
  9. Role of methylated septin 9 as an adjunct diagnostic and prognostic biomarker in hepatocellular carcinoma.
    Title: Role of methylated septin 9 as an adjunct diagnostic and prognostic biomarker in hepatocellular carcinoma.
  10. CircRNA SEPT9 contributes to malignant behaviors of glioma cells via miR-432-5p-mediated regulation of LASP1.
    Title: CircRNA SEPT9 contributes to malignant behaviors of glioma cells via miR-432-5p-mediated regulation of LASP1.
Submit: New GeneRIF Correction See all GeneRIFs (102)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Homology

Clone Names

  • FLJ75490, KIAA0991

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
 PubMed 
enables cadherin binding HDA PubMed 
enables molecular adaptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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
 PubMed 
involved_in positive regulation of non-motile cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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
 PubMed 
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
 PubMed 
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
 PubMed 
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
 PubMed 
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
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

  1. NG_011683.2 RefSeqGene

    Range
    5090..224184
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_370

mRNA and Protein(s)

  1. 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
    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]

  2. 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/Swiss-Prot
    Q9UHD8
    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]

  3. 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
    UniProtKB/Swiss-Prot
    Q9UHD8
    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]

  4. 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/Swiss-Prot
    Q9UHD8
    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]

  5. 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
    Related
    ENSP00000504196.1, ENST00000427180.5
    Conserved Domains (1) summary
    cd01850
    Location:44 → 318
    CDC_Septin; CDC/Septin GTPase family

  6. 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/Swiss-Prot
    Q9UHD8
    Related
    ENSP00000438089.2, ENST00000541152.6
    Conserved Domains (1) summary
    cd01850
    Location:44 → 318
    CDC_Septin; CDC/Septin GTPase family

  7. 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
    UniProtKB/Swiss-Prot
    Q9UHD8
    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]

  8. 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/Swiss-Prot
    Q9UHD8
    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]

  9. 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/Swiss-Prot
    Q9UHD8
    Related
    ENSP00000466247.1, ENST00000591088.5
    Conserved Domains (1) summary
    cd01850
    Location:44 → 318
    CDC_Septin; CDC/Septin GTPase family

  10. 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/Swiss-Prot
    Q9UHD8
    Related
    ENSP00000466648.1, ENST00000592951.5
    Conserved Domains (1) summary
    cd01850
    Location:44 → 318
    CDC_Septin; CDC/Septin GTPase family

  11. 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/Swiss-Prot
    Q9UHD8
    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]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    77281499..77500596
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315955.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    78828..79107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    78174746..78394627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UHD8.2 GenPept UniProtKB/Swiss-Prot:Q9UHD8

Gene LinkOut

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