SPIRE2

spire type actin nucleation factor 2

Basic information

Region (hg38): 16:89818179-89871319

Links

ENSG00000204991

∙ NCBI:84501 ∙ OMIM:609217 ∙ HGNC:30623 ∙ Uniprot:Q8WWL2 ∙ 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 SPIRE2 gene.

not_specified (160 variants)
not_provided (1 variants)
Fanconi_anemia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPIRE2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032451.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			155 clinvar	5 clinvar		160
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	155	6	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPIRE2	protein_coding	protein_coding	ENST00000378247	15	53141

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.44e-9	0.973	125646	0	102	125748	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.259	448	433	1.03	0.0000302	4514
Missense in Polyphen		197	199.73	0.98635		2003
Synonymous	-1.58	215	187	1.15	0.0000136	1476
Loss of Function	2.18	19	32.4	0.587	0.00000169	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000491	0.000486
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000989	0.000816
Finnish	0.000634	0.000416
European (Non-Finnish)	0.000458	0.000448
Middle Eastern	0.000989	0.000816
South Asian	0.000296	0.000294
Other	0.000845	0.000815

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as an actin nucleation factor, remains associated with the slow-growing pointed end of the new filament (PubMed:21620703). Involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport (By similarity). 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 SPIRE1 and SPIRE2, 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:0000250|UniProtKB:Q8K1S6, ECO:0000269|PubMed:21620703, ECO:0000269|PubMed:26287480}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

loftool: 0.735
rvis_EVS: -0.71
rvis_percentile_EVS: 14.78

Haploinsufficiency Scores

pHI: 0.143
hipred: N
hipred_score: 0.197
ghis: 0.570

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.684

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Spire2
Phenotype

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: cytosol;cytoskeleton;cell cortex;cytoplasmic vesicle membrane;cleavage furrow
Molecular function: actin binding