STMN1

protein-coding

stathmin 1, the group of MicroRNA protein coding host genes|Stathmins

Gene summary

This gene belongs to the stathmin family of genes. It encodes a ubiquitous cytosolic phosphoprotein proposed to function as an intracellular relay integrating regulatory signals of the cellular environment. The encoded protein is involved in the regulation of the microtubule filament system by destabilizing microtubules. It prevents assembly and promotes disassembly of microtubules. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

Previous symbols:

LAP18
C1orf215

MANE transcript

NM_005563.4

Inheritance

—

ClinVar variants

U:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr1:25,884,181-25,906,991

External References & Databases

Ensembl (ENSG00000117632)

Transcript & Mutation Effects

hg38 • Region Span ~22.8 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 STMN1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005563.4. 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						0
missense			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	8	0	0	8

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005563.4	RefSeq	NP_005554.1	4	MANE Select
ENST00000455785.7	Ensembl	ENSP00000387858.2	4	MANE Select
NM_001145454.3	RefSeq	NP_001138926.1	4	Standard
NM_203399.2	RefSeq	NP_981944.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

MAPK signaling pathway - Homo sapiens (human)
MicroRNAs in cancer - Homo sapiens (human)
Regulation of Microtubule Cytoskeleton
Retinoblastoma (RB) in Cancer
Rac1-Pak1-p38-MMP-2 pathway

Biological Process

mitotic cytokinesis
microtubule depolymerization
mitotic spindle organization
signal transduction
axonogenesis

Molecular Function

protein binding
tubulin binding

Cellular Component

cytoplasm
cytosol
microtubule
membrane
neuron projection

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000426559
Coding exons: 4
Length: 22811
Individuals with no LoFs: 125674
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125676
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.61	48	91.4	0.525	0.00000489	1138
Missense (PolyPhen)		5	20.789	0.24051		301
Synonymous	0.785	26	31.6	0.822	0.00000153	330
Loss of Function	1.69	3	8.21	0.365	5.31e-7	92

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the regulation of the microtubule (MT) filament system by destabilizing microtubules. Prevents assembly and promotes disassembly of microtubules. Phosphorylation at Ser- 16 may be required for axon formation during neurogenesis. Involved in the control of the learned and innate fear (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.389

Intolerance Scores

LoFtool: 0.0707
RVIS EVS: 0.28
RVIS percentile EVS: 70.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.857

Gene Damage Prediction

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