SPDYE4

speedy/RINGO cell cycle regulator family member E4, the group of Speedy/RINGO cell cycle regulator family

Basic information

Region (hg38): 17:8747524-8758559

Links

ENSG00000183318 ∙ NCBI:388333 ∙ OMIM:617628 ∙ HGNC:35463 ∙ Uniprot:A6NLX3 ∙ 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 SPDYE4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPDYE4 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				1		1
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in SPDYE4

This is a list of pathogenic ClinVar variants found in the SPDYE4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-8753325-T-C		not specified	Uncertain significance (Dec 08, 2023)
17-8753358-C-T		not specified	Uncertain significance (Sep 12, 2023)
17-8753359-G-A		not specified	Uncertain significance (Apr 20, 2024)
17-8753379-T-C		not specified	Uncertain significance (Nov 17, 2022)
17-8753397-A-G		not specified	Uncertain significance (Jun 10, 2024)
17-8753454-G-T		not specified	Uncertain significance (Feb 22, 2023)
17-8753471-C-A		not specified	Uncertain significance (Oct 19, 2024)
17-8755541-C-T		not specified	Uncertain significance (Jan 30, 2024)
17-8755566-C-T		not specified	Uncertain significance (Jun 29, 2022)
17-8755568-G-C		not specified	Uncertain significance (Jan 23, 2024)
17-8755586-A-G		not specified	Uncertain significance (Feb 06, 2025)
17-8756404-C-T		not specified	Uncertain significance (May 06, 2024)
17-8756412-A-G		not specified	Uncertain significance (Aug 20, 2023)
17-8756436-C-T		not specified	Likely benign (Dec 12, 2024)
17-8757318-C-T		not specified	Uncertain significance (Jan 07, 2022)
17-8757337-G-T		not specified	Uncertain significance (Jan 29, 2024)
17-8757347-C-T			Likely benign (Apr 01, 2023)
17-8757376-C-G		not specified	Uncertain significance (Feb 10, 2022)
17-8757381-G-T		not specified	Uncertain significance (Dec 12, 2023)
17-8757384-C-T		not specified	Uncertain significance (Mar 15, 2023)
17-8757424-C-T		not specified	Uncertain significance (Feb 12, 2025)
17-8757460-A-T		not specified	Uncertain significance (Jan 20, 2025)
17-8757465-G-C		not specified	Uncertain significance (Aug 27, 2024)
17-8758304-C-T		not specified	Uncertain significance (Mar 05, 2024)
17-8758310-C-T		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPDYE4	protein_coding	protein_coding	ENST00000328794	6	5454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00157	0.972	125448	0	20	125468	0.0000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.338	132	143	0.921	0.00000902	1531
Missense in Polyphen		17	19.248	0.88322		181
Synonymous	-0.710	66	59.1	1.12	0.00000396	436
Loss of Function	1.95	7	15.2	0.460	9.84e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000940	0.0000940
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000673	0.0000617
Middle Eastern	0.00	0.00
South Asian	0.000242	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.28

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0725

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