SPICE1

spindle and centriole associated protein 1

Basic information

Region (hg38): 3:113442718-113515187

Previous symbols: [ "CCDC52" ]

Links

ENSG00000163611 ∙ NCBI:152185 ∙ OMIM:613447 ∙ HGNC:25083 ∙ Uniprot:Q8N0Z3 ∙ 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 SPICE1 gene.

• not_specified (127 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPICE1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000144718.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			116	11		127
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	116	13	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPICE1	protein_coding	protein_coding	ENST00000295872	17	72470

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.41e-15	0.906	125669	0	79	125748	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.348	439	460	0.954	0.0000247	5570
Missense in Polyphen		132	141.97	0.92978		1772
Synonymous	0.597	149	159	0.940	0.00000810	1663
Loss of Function	2.15	30	45.7	0.656	0.00000237	541

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000587	0.000580
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000437	0.000435
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000301	0.000299
Middle Eastern	0.000437	0.000435
South Asian	0.000366	0.000359
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator required for centriole duplication, for proper bipolar spindle formation and chromosome congression in mitosis. {ECO:0000269|PubMed:20736305}.

Intolerance Scores

• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.66

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.372
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spice1
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of centriole replication;cell division;metaphase plate congression;mitotic spindle assembly
• Cellular component: centrosome;centriole;spindle
• Molecular function: protein binding