SPIRE1

spire type actin nucleation factor 1

Basic information

Region (hg38): 18:12446512-12658107

Links

ENSG00000134278 ∙ NCBI:56907 ∙ OMIM:609216 ∙ HGNC:30622 ∙ Uniprot:Q08AE8 ∙ 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 SPIRE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPIRE1 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			33	1		34
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	34	3	0

Variants in SPIRE1

This is a list of pathogenic ClinVar variants found in the SPIRE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-12449648-C-T		not specified	Likely benign (Sep 08, 2024)
18-12449654-G-T		not specified	Uncertain significance (Feb 17, 2022)
18-12449685-C-G		not specified	Uncertain significance (Dec 19, 2023)
18-12449697-T-C		not specified	Likely benign (May 02, 2023)
18-12449708-T-C		not specified	Uncertain significance (Sep 08, 2024)
18-12449762-C-T		not specified	Uncertain significance (Jun 06, 2023)
18-12452264-C-A		not specified	Uncertain significance (Dec 28, 2023)
18-12452276-C-T		not specified	Uncertain significance (Sep 20, 2023)
18-12452280-G-A		not specified	Uncertain significance (Nov 08, 2022)
18-12452289-T-G		not specified	Uncertain significance (Aug 21, 2023)
18-12452319-C-G		not specified	Uncertain significance (Feb 03, 2022)
18-12452319-C-T		not specified	Uncertain significance (Nov 07, 2024)
18-12452355-T-C		not specified	Uncertain significance (Feb 27, 2023)
18-12454365-G-A		not specified	Uncertain significance (Feb 11, 2022)
18-12454385-T-A		not specified	Uncertain significance (Jul 13, 2021)
18-12463395-C-T		not specified	Uncertain significance (Apr 26, 2023)
18-12463406-G-A		not specified	Uncertain significance (Jan 23, 2023)
18-12463485-T-C		not specified	Uncertain significance (Dec 19, 2023)
18-12464877-T-A		not specified	Uncertain significance (Dec 01, 2022)
18-12464880-A-T		not specified	Uncertain significance (Feb 28, 2024)
18-12464897-G-A		not specified	Uncertain significance (Nov 08, 2024)
18-12479731-T-C		not specified	Uncertain significance (Jun 11, 2021)
18-12479868-A-G		not specified	Uncertain significance (Apr 29, 2024)
18-12485962-A-G		not specified	Uncertain significance (Dec 27, 2023)
18-12485994-C-T		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPIRE1	protein_coding	protein_coding	ENST00000409402	17	211623

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0425	0.958	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	294	374	0.786	0.0000216	4879
Missense in Polyphen		122	179.42	0.67997		2145
Synonymous	-0.0238	140	140	1.00	0.00000809	1484
Loss of Function	4.14	10	37.3	0.268	0.00000192	511

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000798	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an actin nucleation factor, remains associated with the slow-growing pointed end of the new filament (PubMed:11747823, PubMed:21620703). Involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport (PubMed:11747823). Required for asymmetric spindle positioning and asymmetric cell division during meiosis (PubMed:21620703). Required for normal formation of the cleavage furrow and for polar body extrusion during female germ cell meiosis (PubMed:21620703). Also acts in the nucleus: together with FMN2, promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage (PubMed:26287480). {ECO:0000269|PubMed:11747823, ECO:0000269|PubMed:21620703, ECO:0000269|PubMed:26287480}.

Recessive Scores

• pRec: 0.0944

Intolerance Scores

• loftool: 0.668
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.72

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.390
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.759

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spire1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: protein transport;vesicle-mediated transport;actin cytoskeleton organization;cleavage furrow formation;polar body extrusion after meiotic divisions;actin nucleation;intracellular transport;establishment of meiotic spindle localization;formin-nucleated actin cable assembly;positive regulation of double-strand break repair
• Cellular component: nucleoplasm;cytosol;cytoskeleton;cell cortex;cytoplasmic vesicle membrane;cleavage furrow;perinuclear region of cytoplasm
• Molecular function: actin binding