SEPTIN3

protein-coding

septin 3, the group of Septins

Gene summary

This gene belongs to the septin family of GTPases. Members of this family are required for cytokinesis. Expression is upregulated by retinoic acid in a human teratocarcinoma cell line. The specific function of this gene has not been determined. Alternative splicing of this gene results in several transcript variants encoding different isoforms. [provided by RefSeq, May 2018]

Previous symbols:

SEP3
SEPT3

MANE transcript

NM_001363845.2

Inheritance

—

ClinVar variants

U:35B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr22:41,969,443-41,998,221

External References & Databases

Ensembl (ENSG00000100167)

Transcript & Mutation Effects

hg38 • Region Span ~28.8 kb

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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 SEPTIN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001363845.2. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			33 clinvar		1 clinvar	34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	35	1	1	37

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001363845.2	RefSeq	NP_001350774.1	11	MANE Select
ENST00000644076.2	Ensembl	ENSP00000494051.1	11	MANE Select
NM_001389668.1	RefSeq	NP_001376597.1	10	Standard
NM_001389669.1	RefSeq	NP_001376598.1	10	Standard

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

cytoskeleton-dependent cytokinesis

Molecular Function

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

Cellular Component

septin ring
microtubule cytoskeleton
cell junction
septin complex
neuron projection

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396426
Coding exons: 11
Length: 21950
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125748
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.48	113	215	0.525	0.0000122	2381
Missense (PolyPhen)		38	90.724	0.41885		1034
Synonymous	0.0796	80	80.9	0.989	0.00000486	656
Loss of Function	3.14	6	21.8	0.275	0.00000125	239

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.0013	0.0013	notable
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Filament-forming cytoskeletal GTPase (By similarity). May play a role in cytokinesis (Potential). {ECO:0000250, ECO:0000305}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.608
RVIS EVS: -0.3
RVIS percentile EVS: 32.62

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.381

Gene Damage Prediction

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