SPDYE1

speedy/RINGO cell cycle regulator family member E1, the group of Speedy/RINGO cell cycle regulator family

Basic information

Region (hg38): 7:43997897-44010124

Previous symbols: [ "WBSCR19" ]

Links

ENSG00000136206 ∙ NCBI:285955 ∙ OMIM:617623 ∙ HGNC:16408 ∙ Uniprot:Q8NFV5 ∙ 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 SPDYE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPDYE1 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			54			54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	0	0

Variants in SPDYE1

This is a list of pathogenic ClinVar variants found in the SPDYE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-44001081-C-A		not specified	Uncertain significance (Dec 09, 2023)
7-44001092-T-C		not specified	Uncertain significance (Mar 30, 2024)
7-44001146-G-A		not specified	Uncertain significance (Aug 16, 2022)
7-44001150-C-G		not specified	Uncertain significance (Aug 08, 2023)
7-44001161-C-T		not specified	Uncertain significance (Jan 16, 2025)
7-44001173-C-A		not specified	Uncertain significance (Jun 07, 2024)
7-44001246-T-C		not specified	Uncertain significance (Oct 05, 2023)
7-44002592-C-G		not specified	Uncertain significance (Feb 22, 2023)
7-44002596-G-A		not specified	Uncertain significance (May 09, 2023)
7-44002629-G-A		not specified	Uncertain significance (Dec 17, 2023)
7-44002658-A-G		not specified	Uncertain significance (Sep 12, 2023)
7-44002670-T-G		not specified	Uncertain significance (Jun 22, 2021)
7-44002686-G-C		not specified	Uncertain significance (May 23, 2023)
7-44002712-G-A		not specified	Uncertain significance (Dec 31, 2024)
7-44002716-T-C		not specified	Uncertain significance (Jan 05, 2022)
7-44002749-T-C		not specified	Uncertain significance (Dec 12, 2024)
7-44002761-G-A		not specified	Uncertain significance (May 04, 2023)
7-44002764-G-A		not specified	Uncertain significance (May 04, 2023)
7-44002796-G-A		not specified	Uncertain significance (Apr 17, 2023)
7-44002800-C-T		not specified	Uncertain significance (May 17, 2023)
7-44005151-G-C		not specified	Uncertain significance (Nov 07, 2023)
7-44005176-G-A		not specified	Uncertain significance (Sep 08, 2024)
7-44005176-G-T		not specified	Uncertain significance (Dec 22, 2023)
7-44005209-T-G		not specified	Uncertain significance (Mar 06, 2023)
7-44007276-C-G		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPDYE1	protein_coding	protein_coding	ENST00000258704	6	9234

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.55e-11	0.0915	125648	0	99	125747	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.459	208	190	1.09	0.0000132	2193
Missense in Polyphen		46	49.836	0.92302		692
Synonymous	-1.03	83	71.9	1.15	0.00000459	612
Loss of Function	0.337	17	18.6	0.915	0.00000119	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00121
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000617	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000321	0.000308
Middle Eastern	0.000617	0.000598
South Asian	0.000530	0.000523
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=SPDYE1 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region (PubMed:12073013). {ECO:0000269|PubMed:12073013}.
• Pathway: Oocyte meiosis - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• pHI: 0.0935
• hipred: N
• hipred_score: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0351

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