STMN4

stathmin 4, the group of Stathmins

Basic information

Region (hg38): 8:27235308-27258420

Links

ENSG00000015592 ∙ NCBI:81551 ∙ ∙ HGNC:16078 ∙ Uniprot:Q9H169 ∙ 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 STMN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STMN4 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					2	2
missense			10	1		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	10	1	2

Variants in STMN4

This is a list of pathogenic ClinVar variants found in the STMN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-27236882-C-T			Benign (Jul 19, 2018)
8-27239964-C-T			Likely benign (Feb 27, 2018)
8-27239987-T-C		not specified	Uncertain significance (Jul 12, 2023)
8-27239988-C-G		not specified	Uncertain significance (Jul 22, 2024)
8-27240069-T-C		not specified	Uncertain significance (Jan 26, 2025)
8-27240089-A-G		not specified	Uncertain significance (Jan 16, 2024)
8-27241150-A-C		not specified	Uncertain significance (Jun 16, 2024)
8-27241159-G-C			Benign (Jul 31, 2018)
8-27241251-C-T		not specified	Uncertain significance (Feb 28, 2024)
8-27241256-G-A		not specified	Uncertain significance (Dec 15, 2022)
8-27241740-A-G		not specified	Uncertain significance (Aug 14, 2023)
8-27242412-A-G		not specified	Uncertain significance (May 31, 2022)
8-27242432-G-T		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STMN4	protein_coding	protein_coding	ENST00000350889	6	23098

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0908	0.901	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	82	126	0.650	0.00000743	1428
Missense in Polyphen		20	47.918	0.41738		548
Synonymous	-0.0173	56	55.8	1.00	0.00000379	383
Loss of Function	2.32	4	13.1	0.307	7.22e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits microtubule-destabilizing activity. {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.340
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.190
• hipred: Y
• hipred_score: 0.618
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.755

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stmn4

Zebrafish Information Network

• Gene name: stmn4
• Affected structure: cell population proliferation
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: microtubule depolymerization;regulation of microtubule polymerization or depolymerization;neuron projection development;regulation of cytoskeleton organization
• Cellular component: cytoplasm;Golgi apparatus;growth cone;neuron projection
• Molecular function: tubulin binding