SPDYA

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

Basic information

Region (hg38): 2:28782517-28850611

Previous symbols: [ "SPDY1" ]

Links

ENSG00000163806 ∙ NCBI:245711 ∙ OMIM:614029 ∙ HGNC:30613 ∙ Uniprot:Q5MJ70 ∙ 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 SPDYA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPDYA 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			9	1	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	13	1	1

Variants in SPDYA

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

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

Position	Type	Phenotype	Significance	ClinVar
2-28783650-G-A			Benign (Oct 16, 2018)
2-28783714-G-A			Likely benign (Jun 06, 2019)
2-28783725-G-C			Benign (Oct 01, 2018)
2-28783757-G-GA			Benign (Aug 12, 2019)
2-28783890-C-T			Likely benign (Apr 07, 2023)
2-28783893-C-G			Likely benign (Mar 07, 2023)
2-28783893-C-T			Likely benign (Mar 26, 2023)
2-28783895-T-G			Likely benign (Apr 28, 2022)
2-28783899-A-G			Likely benign (Jul 17, 2021)
2-28783900-T-C			Likely benign (Mar 29, 2023)
2-28783902-T-G			Likely benign (Jul 29, 2022)
2-28783909-T-C			Likely benign (Jul 29, 2023)
2-28783923-G-A			Likely benign (Apr 08, 2022)
2-28783923-G-T		Cardiovascular phenotype	Likely benign (Aug 31, 2021)
2-28783925-A-C			Uncertain significance (Sep 10, 2023)
2-28783930-A-G		Noonan syndrome	Uncertain significance (Feb 03, 2023)
2-28783931-T-A		Noonan syndrome • Noonan syndrome-like disorder with loose anagen hair 2	Conflicting classifications of pathogenicity (Jan 07, 2022)
2-28783934-A-C		Noonan syndrome-like disorder with loose anagen hair 2 • Cardiovascular phenotype	Pathogenic (Dec 11, 2023)
2-28783934-A-T		Noonan syndrome-like disorder with loose anagen hair 2	Pathogenic (Sep 08, 2016)
2-28783948-A-G			Uncertain significance (Aug 07, 2022)
2-28783979-G-GT			Uncertain significance (Mar 19, 2023)
2-28783992-G-C			Likely benign (Sep 26, 2023)
2-28783996-TTTAA-T			Likely benign (Oct 13, 2023)
2-28784096-C-T			Likely benign (Oct 24, 2018)
2-28784117-C-T			Likely benign (Mar 17, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPDYA	protein_coding	protein_coding	ENST00000334056	6	68095

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.551	0.448	125705	0	23	125728	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	105	161	0.653	0.00000798	2063
Missense in Polyphen		26	55.403	0.46929		708
Synonymous	0.568	47	52.2	0.900	0.00000246	548
Loss of Function	2.92	3	15.3	0.196	7.29e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000224	0.000223
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000721	0.0000703
Middle Eastern	0.000114	0.000109
South Asian	0.000201	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the G1/S phase transition of the cell cycle by binding and activating CDK1 and CDK2 (PubMed:12972555). Contributes to CDK2 activation without promoting CDK2 phosphorylation, by inducing a conformation change of the CDK2 T- loop that obstructs the substrate-binding cleft prior to kinase activation (PubMed:28666995). Mediates cell survival during the DNA damage process through activation of CDK2 (PubMed:12839962). {ECO:0000269|PubMed:11980914, ECO:0000269|PubMed:12839962, ECO:0000269|PubMed:12972555, ECO:0000269|PubMed:28666995}.
• Pathway: Oocyte meiosis - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0839

Intolerance Scores

• loftool: 0.347
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.0611
• hipred: Y
• hipred_score: 0.730

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.812

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spdya
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;cellular response to DNA damage stimulus;male meiotic nuclear division;multicellular organism development;positive regulation of cell population proliferation;activation of protein kinase activity;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of protein kinase activity
• Cellular component: nucleus;nucleoplasm
• Molecular function: protein kinase binding;protein kinase activator activity