SEPTIN10

protein-coding

septin 10, the group of Septins

Gene summary

This gene encodes a member of the septin family of cytoskeletal proteins with GTPase activity. This protein localizes to the cytoplasm and nucleus and displays GTP-binding and GTPase activity. A pseudogene for this gene is located on chromosome 8. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2012]

Previous symbols:

SEPT10

MANE transcript

NM_144710.5

Inheritance

—

ClinVar variants

U:119B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr2:109,542,799-109,614,143

External References & Databases

Ensembl (ENSG00000186522)

Transcript & Mutation Effects

hg38 • Region Span ~71.3 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 SEPTIN10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144710.5. 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			2 clinvar	1 clinvar		3
missense			111 clinvar	2 clinvar		113
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	119	3	0	122

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 113 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144710.5	RefSeq	NP_653311.1	11	MANE Select
ENST00000397712.7	Ensembl	ENSP00000380824.2	11	MANE Select
NM_001321496.2	RefSeq	NP_001308425.1	8	Standard
NM_001321498.2	RefSeq	NP_001308427.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cytoskeleton-dependent cytokinesis

Molecular Function

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

Cellular Component

septin ring
microtubule cytoskeleton
septin complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397712
Coding exons: 11
Length: 71225
Individuals with no LoFs: 124719
Homozygous LoFs: 0
Heterozygous LoFs: 76
Defined: 124795
p: 0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.14	285	236	1.21	0.0000123	3032
Missense (PolyPhen)		150	98.749	1.519		1244
Synonymous	1.06	68	80.1	0.849	0.00000419	782
Loss of Function	0.953	17	21.8	0.780	0.00000109	285

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00019	rare
Latino/Admixed American	0.00062	0.00058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00037	0.00036	rare
South Asian	0.00023	0.00023	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.698
RVIS EVS: -0.29
RVIS percentile EVS: 33.42

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.169

Gene Damage Prediction

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