STMN3

stathmin 3, the group of Stathmins

Basic information

Region (hg38): 20:63639705-63657682

Links

ENSG00000197457 ∙ NCBI:50861 ∙ OMIM:608362 ∙ HGNC:15926 ∙ Uniprot:Q9NZ72 ∙ 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 STMN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STMN3 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in STMN3

This is a list of pathogenic ClinVar variants found in the STMN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63641351-T-C		not specified	Uncertain significance (Jan 10, 2023)
20-63642113-C-G		not specified	Uncertain significance (Jan 24, 2025)
20-63642124-T-G		not specified	Uncertain significance (Jan 20, 2025)
20-63642134-C-A		not specified	Uncertain significance (Feb 08, 2023)
20-63642139-A-C		not specified	Uncertain significance (Feb 05, 2024)
20-63642243-C-G		not specified	Uncertain significance (Mar 14, 2025)
20-63642257-C-T		not specified	Uncertain significance (Feb 18, 2025)
20-63643798-C-A		not specified	Uncertain significance (Nov 08, 2022)
20-63643865-G-A		not specified	Uncertain significance (May 17, 2023)
20-63643872-T-C		not specified	Uncertain significance (Mar 29, 2022)
20-63643895-C-T		not specified	Uncertain significance (May 25, 2022)
20-63643904-C-T		not specified	Uncertain significance (Nov 28, 2024)
20-63644271-G-A		not specified	Uncertain significance (Feb 28, 2023)
20-63653331-A-C		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STMN3	protein_coding	protein_coding	ENST00000370053	5	13720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0839	0.876	125350	0	4	125354	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	65	103	0.629	0.00000570	1153
Missense in Polyphen		19	34.411	0.55214		333
Synonymous	-0.141	48	46.8	1.03	0.00000277	336
Loss of Function	1.75	3	8.51	0.353	3.61e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000591	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits microtubule-destabilizing activity, which is antagonized by STAT3. {ECO:0000250}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.109
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.399
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.527

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stmn3

Gene ontology

• Biological process: blastocyst hatching;microtubule depolymerization;nervous system development;regulation of microtubule polymerization or depolymerization;cytoplasmic microtubule organization;neuron projection development;negative regulation of Rac protein signal transduction;regulation of GTPase activity;regulation of cytoskeleton organization
• Cellular component: cytoplasm;Golgi apparatus;growth cone;neuron projection
• Molecular function: tubulin binding;protein domain specific binding