SPDYE2B

speedy/RINGO cell cycle regulator family member E2B, the group of Speedy/RINGO cell cycle regulator family

Basic information

Region (hg38): 7:102650319-102662625

Links

ENSG00000173678 ∙ NCBI:100310812 ∙ ∙ HGNC:48334 ∙ Uniprot:A6NHP3 ∙ 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 SPDYE2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPDYE2B 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			1	1		2
nonsense						0
start loss				1		1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	3	0

Variants in SPDYE2B

This is a list of pathogenic ClinVar variants found in the SPDYE2B region.

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

Position	Type	Phenotype	Significance	ClinVar
7-102653549-G-A		not specified	Likely benign (Jul 09, 2021)
7-102653583-T-C		not specified	Likely benign (Jan 04, 2025)
7-102653611-G-A			Likely benign (Nov 01, 2023)
7-102655038-T-C		not specified	Likely benign (May 11, 2022)
7-102656299-C-T		not specified	Uncertain significance (Feb 21, 2025)
7-102657580-C-G		not specified	Uncertain significance (Nov 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPDYE2B	protein_coding	protein_coding	ENST00000507450	7	11076

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.376	0.488	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.287	3	4.76	0.630	2.03e-7	2629
Missense in Polyphen		2	0.95446	2.0954		1000
Synonymous	0.948	0	1.46	0.00	6.32e-8	735
Loss of Function	0.857	0	0.856	0.00	3.65e-8	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• ghis: 0.420

Essentials

• essential_gene_CRISPR: N

Gene ontology

• Molecular function: protein kinase binding