SPDYE3

speedy/RINGO cell cycle regulator family member E3, the group of Speedy/RINGO cell cycle regulator family

Basic information

Region (hg38): 7:100307701-100322196

Links

ENSG00000214300 ∙ NCBI:441272 ∙ OMIM:617625 ∙ HGNC:35462 ∙ Uniprot:A6NKU9 ∙ 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 SPDYE3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPDYE3 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			58	2		60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	2	0

Variants in SPDYE3

This is a list of pathogenic ClinVar variants found in the SPDYE3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100307890-C-T		not specified	Uncertain significance (Nov 09, 2023)
7-100307926-C-T		not specified	Uncertain significance (Jun 17, 2024)
7-100307932-G-A		not specified	Uncertain significance (Nov 12, 2021)
7-100307938-C-T		not specified	Uncertain significance (Jan 23, 2024)
7-100307980-C-T		not specified	Uncertain significance (Dec 09, 2023)
7-100308977-C-G		not specified	Uncertain significance (Dec 06, 2022)
7-100308985-G-T		not specified	Uncertain significance (Jun 14, 2022)
7-100308998-C-T		not specified	Uncertain significance (Dec 18, 2023)
7-100309000-C-T		not specified	Likely benign (Feb 03, 2022)
7-100309001-G-A		not specified	Uncertain significance (Feb 23, 2023)
7-100309130-C-T		not specified	Uncertain significance (Dec 20, 2021)
7-100309136-G-A		not specified	Uncertain significance (Aug 15, 2023)
7-100310398-G-A		not specified	Uncertain significance (Sep 16, 2021)
7-100310420-G-A		not specified	Uncertain significance (Aug 02, 2022)
7-100310474-A-G		not specified	Uncertain significance (Jun 07, 2024)
7-100310486-C-T		not specified	Uncertain significance (May 20, 2024)
7-100310557-G-C		not specified	Uncertain significance (Mar 01, 2023)
7-100311771-C-A		not specified	Uncertain significance (Dec 08, 2023)
7-100311861-A-C		not specified	Uncertain significance (Dec 28, 2022)
7-100311924-C-T		not specified	Uncertain significance (May 11, 2022)
7-100311947-G-A		not specified	Uncertain significance (Mar 19, 2024)
7-100311960-G-A		not specified	Uncertain significance (Sep 01, 2021)
7-100313164-C-A		not specified	Uncertain significance (May 26, 2024)
7-100313164-C-T		not specified	Uncertain significance (Apr 11, 2023)
7-100313166-C-T		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPDYE3	protein_coding	protein_coding	ENST00000332397	10	14495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000151	0.880	125638	0	32	125670	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.625	166	145	1.15	0.00000929	3445
Missense in Polyphen		44	39.685	1.1087		931
Synonymous	0.0228	55	55.2	0.996	0.00000341	1007
Loss of Function	1.42	8	13.6	0.586	6.64e-7	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000175	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00105	0.000979
Finnish	0.0000644	0.0000462
European (Non-Finnish)	0.0000544	0.0000528
Middle Eastern	0.00105	0.000979
South Asian	0.000109	0.0000980
Other	0.000182	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Oocyte meiosis - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.348
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0598

Gene Damage Prediction

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

Gene ontology

• Molecular function: protein kinase binding