SEPTIN4

septin 4, the group of Septins

Basic information

Region (hg38): 17:58520250-58544368

Previous symbols: [ "PNUTL2", "C17orf47", "SEPT4" ]

Links

ENSG00000108387 ∙ NCBI:5414 ∙ OMIM:603696 ∙ HGNC:9165 ∙ Uniprot:O43236 ∙ 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 SEPTIN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN4 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				1		1
missense			30	3	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	4	1

Variants in SEPTIN4

This is a list of pathogenic ClinVar variants found in the SEPTIN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-58520449-T-C		not specified	Uncertain significance (Aug 16, 2021)
17-58520472-T-A		not specified	Uncertain significance (Jun 24, 2022)
17-58520475-A-G		not specified	Uncertain significance (Oct 25, 2022)
17-58520745-C-T			Benign (Apr 26, 2018)
17-58520759-C-T		not specified	Uncertain significance (Aug 04, 2023)
17-58520832-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-58520839-T-G		not specified	Uncertain significance (Sep 14, 2022)
17-58521025-C-T		not specified	Uncertain significance (Dec 21, 2023)
17-58521053-G-A		not specified	Uncertain significance (Apr 13, 2022)
17-58521067-T-C		not specified	Uncertain significance (Mar 24, 2023)
17-58521143-A-G		not specified	Uncertain significance (Feb 27, 2023)
17-58521149-C-A		not specified	Uncertain significance (Jul 05, 2023)
17-58521328-A-G		not specified	Uncertain significance (Feb 17, 2024)
17-58521616-T-C		not specified	Uncertain significance (Feb 14, 2023)
17-58521633-A-G		not specified	Uncertain significance (Apr 13, 2022)
17-58522051-C-T		not specified	Uncertain significance (May 06, 2024)
17-58522088-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-58525121-C-A		not specified	Uncertain significance (May 24, 2023)
17-58525133-G-A		not specified	Uncertain significance (Jul 13, 2022)
17-58525162-A-G		not specified	Uncertain significance (Apr 08, 2023)
17-58525714-C-T			Likely benign (Apr 17, 2018)
17-58525722-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-58525752-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-58526304-C-G		not specified	Uncertain significance (May 09, 2023)
17-58526791-C-G		not specified	Uncertain significance (Oct 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPTIN4	protein_coding	protein_coding	ENST00000457347	13	20569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000166	0.999	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	222	287	0.774	0.0000173	3249
Missense in Polyphen		70	108.43	0.64559		1240
Synonymous	1.35	87	105	0.832	0.00000552	954
Loss of Function	2.83	11	26.8	0.411	0.00000164	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000113	0.000109
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Filament-forming cytoskeletal GTPase (By similarity). May play a role in cytokinesis (Potential). 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). May play a role in platelet secretion. Isoform ARTS, but not the other isoforms, is required for the induction of cell death mediated by TGF-beta and by other apoptotic stimuli. {ECO:0000250, ECO:0000269|PubMed:11146656, ECO:0000269|PubMed:15029247, ECO:0000269|PubMed:15116257, ECO:0000269|PubMed:15837787, ECO:0000269|PubMed:9889007, ECO:0000305, ECO:0000305|PubMed:25588830}.
• Pathway: Apoptosis - multiple species - Homo sapiens (human);Apoptosis - Homo sapiens (human);Apoptosis Modulation and Signaling (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.905
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.624
• hipred: Y
• hipred_score: 0.694
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sept4
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: apoptotic process;brain development;regulation of exocytosis;sperm mitochondrion organization;positive regulation of protein ubiquitination;regulation of apoptotic process;positive regulation of apoptotic process;sperm capacitation;protein homooligomerization;cytoskeleton-dependent cytokinesis;positive regulation of intrinsic apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm;mitochondrion;septin ring;synaptic vesicle;microtubule cytoskeleton;septin complex;myelin sheath;sperm annulus
• Molecular function: magnesium ion binding;GTPase activity;structural molecule activity;protein binding;GTP binding;protein-containing complex scaffold activity;protein homodimerization activity