STMN2

stathmin 2, the group of Stathmins

Basic information

Region (hg38): 8:79611116-79666158

Previous symbols: [ "SCGN10" ]

Links

ENSG00000104435 ∙ NCBI:11075 ∙ OMIM:600621 ∙ HGNC:10577 ∙ Uniprot:Q93045 ∙ 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 STMN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STMN2 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	3	0	0

Variants in STMN2

This is a list of pathogenic ClinVar variants found in the STMN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-79641529-G-C		not specified	Uncertain significance (Nov 15, 2021)
8-79654923-G-A		not specified	Uncertain significance (Dec 13, 2022)
8-79663622-T-C		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STMN2	protein_coding	protein_coding	ENST00000518111	5	55362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0231	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	50	96.7	0.517	0.00000517	1222
Missense in Polyphen		13	26.246	0.49532		352
Synonymous	-0.482	39	35.4	1.10	0.00000189	338
Loss of Function	3.15	0	11.6	0.00	6.45e-7	138

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of microtubule stability. When phosphorylated by MAPK8, stabilizes microtubules and consequently controls neurite length in cortical neurons. In the developing brain, negatively regulates the rate of exit from multipolar stage and retards radial migration from the ventricular zone (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.250

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.961
• hipred: Y
• hipred_score: 0.714
• ghis: 0.653

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Stmn2

Gene ontology

• Biological process: microtubule depolymerization;negative regulation of microtubule depolymerization;positive regulation of neuron projection development;negative regulation of neuron projection development;regulation of microtubule polymerization or depolymerization;negative regulation of microtubule polymerization;positive regulation of microtubule depolymerization;neuron projection development;regulation of cytoskeleton organization;cellular response to nerve growth factor stimulus
• Cellular component: cytoplasm;endosome;Golgi apparatus;membrane;lamellipodium;growth cone;neuron projection;neuronal cell body;perinuclear region of cytoplasm
• Molecular function: protein binding;tubulin binding;calcium-dependent protein binding