SPDYA

protein-coding

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

Gene summary

Enables protein kinase activator activity and protein kinase binding activity. Involved in DNA damage response; G1/S transition of mitotic cell cycle; and positive regulation of cell population proliferation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SPDY1

MANE transcript

NM_182756.4

Inheritance

—

ClinVar variants

U:22B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr2:28,782,517-28,850,611

External References & Databases

Ensembl (ENSG00000163806)

Transcript & Mutation Effects

hg38 • Region Span ~68.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPDYA variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182756.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			20 clinvar	2 clinvar	1 clinvar	23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	22	2	1	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182756.4	RefSeq	NP_877433.2	6	MANE Select
ENST00000334056.10	Ensembl	ENSP00000335628.5	6	MANE Select
NM_001008779.1	RefSeq	NP_001008779.1	5	Standard
NM_001142634.2	RefSeq	NP_001136106.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Oocyte meiosis - Homo sapiens (human)
Progesterone-mediated oocyte maturation - Homo sapiens (human)

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

Molecular Function

protein kinase binding
protein kinase activator activity

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334056
Coding exons: 6
Length: 68095
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125728
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.56	105	161	0.653	0.00000798	2063
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00010	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0839

Intolerance Scores

LoFtool: 0.347
RVIS EVS: 0.1
RVIS percentile EVS: 61.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.812

Gene Damage Prediction

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