SEPTIN9

septin 9, the group of Septins

Basic information

Region (hg38): 17:77280568-77500596

Previous symbols: [ "MSF", "SEPT9" ]

Links

ENSG00000184640 ∙ NCBI:10801 ∙ OMIM:604061 ∙ HGNC:7323 ∙ Uniprot:Q9UHD8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyotrophic neuralgia (Strong), mode of inheritance: AD
• neuralgic amyotrophy (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amyotrophy, hereditary neuralgic	AD	Neurologic	It has been reported that medical treatment (eg, with corticosteroids) may prevent attacks of brachial plexus neuropathy during specific situations, such as during surgery and in childbirth	Craniofacial; Neurologic	11739810; 16186812; 18492087; 19451530; 19939853; 20301569; 23042485

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEPTIN9 gene.

• not provided (429 variants)
• Amyotrophic neuralgia (127 variants)
• not specified (15 variants)
• Hereditary Neuralgic Amyotrophy (HNA) (12 variants)
• Inborn genetic diseases (11 variants)
• Charcot-Marie-Tooth disease (3 variants)
• SEPTIN9-related condition (2 variants)
• Charcot-Marie-Tooth disease, type I (2 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN9 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	76	12	90
missense			125	8	5	138
nonsense						0
start loss			1			1
frameshift			3			3
inframe indel			3			3
splice donor/acceptor (+/-2bp)			1			1
splice region			11	12	4	27
non coding	1		54	84	104	243
Total	1	0	189	168	121

Variants in SEPTIN9

This is a list of pathogenic ClinVar variants found in the SEPTIN9 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-77281145-G-T			Benign (Jul 15, 2018)
17-77281348-C-G			Benign (Jul 15, 2018)
17-77281351-T-G			Benign (Jul 21, 2018)
17-77281386-G-T			Benign (Aug 06, 2019)
17-77281498-C-T			Likely benign (Aug 07, 2018)
17-77281529-A-C		SEPTIN9-related disorder	Benign (Oct 28, 2019)
17-77281555-GT-G		not specified	Uncertain significance (Oct 24, 2022)
17-77281643-C-T			Likely benign (Aug 07, 2018)
17-77281807-C-G			Likely benign (Aug 30, 2018)
17-77281874-G-A			Likely benign (Jul 31, 2018)
17-77281875-C-G			Likely benign (Feb 24, 2019)
17-77286383-C-A		Charcot-Marie-Tooth disease	Uncertain significance (Aug 14, 2019)
17-77306862-G-T			Likely benign (Jul 26, 2019)
17-77307020-G-A			Benign (Jul 17, 2018)
17-77307076-T-C			Likely benign (Jul 26, 2019)
17-77307147-C-T			Uncertain significance (Jan 01, 2017)
17-77307149-C-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
17-77307153-C-T		Inborn genetic diseases	Uncertain significance (Feb 08, 2023)
17-77307168-T-A		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
17-77307171-G-A			Uncertain significance (Mar 01, 2023)
17-77307174-G-C		Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
17-77307216-T-C			Benign (Jul 06, 2018)
17-77307420-G-A			Benign (Jul 17, 2018)
17-77307433-G-C			Likely benign (Aug 07, 2018)
17-77319217-T-C			Benign (Jul 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN9	protein_coding	protein_coding	ENST00000427177	12	220028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00421	124588	0	2	124590	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.62	302	392	0.770	0.0000281	3800
Missense in Polyphen		78	148.04	0.5269		1444
Synonymous	-1.85	198	168	1.18	0.0000134	1165
Loss of Function	4.26	2	25.0	0.0801	0.00000126	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000890	0.00000885
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 (By similarity). May play a role in cytokinesis (Potential). May play a role in the internalization of 2 intracellular microbial pathogens, Listeria monocytogenes and Shigella flexneri. {ECO:0000250, ECO:0000305}.
• Disease: DISEASE: Hereditary neuralgic amyotrophy (HNA) [MIM:162100]: Autosomal dominant form of recurrent focal neuropathy characterized clinically by acute, recurrent episodes of brachial plexus neuropathy with muscle weakness and atrophy preceded by severe pain in the affected arm. HNA is triggered by environmental factors such as infection or parturition. {ECO:0000269|PubMed:16186812, ECO:0000269|PubMed:17546647, ECO:0000269|PubMed:18492087, ECO:0000269|PubMed:19451530}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Bacterial invasion of epithelial cells - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.759
• rvis_EVS: -1.5
• rvis_percentile_EVS: 3.57

Haploinsufficiency Scores

• pHI: 0.339
• hipred: Y
• hipred_score: 0.775
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept9
• Phenotype: immune system phenotype; normal 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); hematopoietic system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: sept9a
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: protein heterooligomerization;cytoskeleton-dependent cytokinesis;positive regulation of non-motile cilium assembly
• Cellular component: stress fiber;cytoplasm;microtubule;axoneme;septin ring;actin cytoskeleton;microtubule cytoskeleton;septin complex;perinuclear region of cytoplasm;non-motile cilium
• Molecular function: GTPase activity;protein binding;GTP binding;protein-containing complex scaffold activity;cadherin binding