STMND1

stathmin domain containing 1

Basic information

Region (hg38): 6:17102049-17131378

Links

ENSG00000230873 ∙ NCBI:401236 ∙ ∙ HGNC:44668 ∙ Uniprot:H3BQB6 ∙ 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 STMND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STMND1 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			16	3		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	3	0

Variants in STMND1

This is a list of pathogenic ClinVar variants found in the STMND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-17102262-G-A		not specified	Uncertain significance (Apr 17, 2024)
6-17115005-G-A		not specified	Likely benign (Apr 06, 2023)
6-17115062-T-G		not specified	Uncertain significance (Nov 10, 2022)
6-17120655-G-A		not specified	Uncertain significance (Feb 17, 2024)
6-17120661-G-A		not specified	Uncertain significance (Jun 09, 2022)
6-17120710-A-G		not specified	Uncertain significance (Jul 14, 2021)
6-17120727-T-C		not specified	Uncertain significance (Jan 23, 2023)
6-17129119-C-T		not specified	Uncertain significance (Mar 13, 2023)
6-17129171-C-G		not specified	Uncertain significance (Jan 23, 2024)
6-17129194-C-T		not specified	Uncertain significance (Feb 05, 2024)
6-17129208-G-A		not specified	Likely benign (Apr 05, 2023)
6-17129229-G-A		not specified	Uncertain significance (Mar 29, 2022)
6-17129232-G-A		not specified	Uncertain significance (Jun 17, 2024)
6-17130605-A-T		not specified	Uncertain significance (Dec 26, 2023)
6-17130625-G-A		not specified	Likely benign (Oct 19, 2021)
6-17130640-T-C		not specified	Uncertain significance (May 30, 2023)
6-17130693-T-C		not specified	Uncertain significance (Apr 08, 2022)
6-17130750-G-A		not specified	Uncertain significance (Dec 15, 2022)
6-17130754-G-A		not specified	Uncertain significance (Mar 17, 2023)
6-17130810-G-C		not specified	Uncertain significance (Aug 04, 2021)
6-17130825-T-G		not specified	Uncertain significance (Jan 09, 2023)
6-17130866-T-A		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STMND1	protein_coding	protein_coding	ENST00000536551	5	29115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000987	0.589	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.791	104	129	0.804	0.00000666	1790
Missense in Polyphen		26	31.702	0.82015		520
Synonymous	2.39	27	48.1	0.561	0.00000247	523
Loss of Function	0.664	7	9.17	0.763	5.96e-7	120

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

Haploinsufficiency Scores

• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stmnd1

Gene ontology

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