SFI1

SFI1 centrin binding protein, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 22:31488687-31618588

Links

ENSG00000198089 ∙ NCBI:9814 ∙ OMIM:612765 ∙ HGNC:29064 ∙ Uniprot:A8K8P3 ∙ 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 SFI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFI1 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			100	19	3	122
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	100	21	3

Variants in SFI1

This is a list of pathogenic ClinVar variants found in the SFI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-31488697-C-A			Uncertain significance (Apr 01, 2021)
22-31508318-A-T		not specified	Uncertain significance (Mar 02, 2023)
22-31508367-T-C		not specified	Uncertain significance (Nov 22, 2023)
22-31528757-G-T		not specified	Uncertain significance (Apr 07, 2022)
22-31528760-T-C		not specified	Uncertain significance (Apr 28, 2023)
22-31528772-C-T		not specified	Uncertain significance (Aug 13, 2021)
22-31528773-G-C		not specified	Uncertain significance (Nov 15, 2023)
22-31528788-G-T		not specified	Uncertain significance (Dec 20, 2021)
22-31528812-G-A			Benign (Jul 13, 2018)
22-31528823-A-G		not specified	Likely benign (Jul 29, 2023)
22-31528841-C-T		not specified	Uncertain significance (Aug 04, 2023)
22-31528857-G-T		not specified	Uncertain significance (Sep 06, 2022)
22-31531059-T-G		not specified	Uncertain significance (Jun 23, 2021)
22-31531085-A-T		not specified	Uncertain significance (Dec 21, 2023)
22-31546869-A-G		not specified	Uncertain significance (Dec 06, 2021)
22-31546878-G-A		not specified	Likely benign (May 03, 2023)
22-31546908-A-C		not specified	Uncertain significance (Aug 21, 2023)
22-31546912-G-C		not specified	Uncertain significance (Apr 25, 2023)
22-31546936-G-T		not specified	Uncertain significance (May 30, 2022)
22-31550246-C-T			Likely benign (Oct 01, 2022)
22-31550300-C-T		not specified	Uncertain significance (Mar 25, 2024)
22-31550301-G-A		not specified	Likely benign (Sep 26, 2022)
22-31550310-A-G		not specified	Likely benign (Jun 11, 2021)
22-31556979-G-T		not specified	Uncertain significance (Jul 15, 2021)
22-31557058-C-T		not specified	Likely benign (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFI1	protein_coding	protein_coding	ENST00000400288	32	129899

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.94e-44	0.000152	123849	5	974	124828	0.00393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.543	760	719	1.06	0.0000452	7980
Missense in Polyphen		213	194.1	1.0974		2629
Synonymous	0.0267	267	268	0.998	0.0000149	2381
Loss of Function	1.43	75	89.6	0.837	0.00000481	879

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00593	0.00578
Ashkenazi Jewish	0.00229	0.00229
East Asian	0.00195	0.00195
Finnish	0.00819	0.00806
European (Non-Finnish)	0.00391	0.00383
Middle Eastern	0.00195	0.00195
South Asian	0.00531	0.00524
Other	0.00489	0.00462

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the dynamic structure of centrosome- associated contractile fibers via its interaction with CETN2. {ECO:0000269|PubMed:16956364}.
• Pathway: Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.0911

Intolerance Scores

• loftool: 0.986
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.53

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.425
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.767

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Sfi1

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;regulation of G2/M transition of mitotic cell cycle;negative regulation of phosphatase activity;ciliary basal body-plasma membrane docking
• Cellular component: centrosome;centriole;cytosol
• Molecular function: protein binding;phosphatase binding