SPDYC

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

Basic information

Region (hg38): 11:65170233-65173374

Links

ENSG00000204710 ∙ NCBI:387778 ∙ OMIM:614030 ∙ HGNC:32681 ∙ Uniprot:Q5MJ68 ∙ 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 SPDYC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPDYC 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			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			3			3
Total	0	0	26	3	0

Variants in SPDYC

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

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

Position	Type	Phenotype	Significance	ClinVar
11-65170239-C-T		not specified	Uncertain significance (Nov 09, 2023)
11-65170248-A-G		not specified	Uncertain significance (Oct 13, 2023)
11-65170251-C-T		not specified	Uncertain significance (Jul 12, 2022)
11-65170260-G-A		not specified	Likely benign (Aug 20, 2024)
11-65171386-C-T		not specified	Uncertain significance (Mar 13, 2023)
11-65171401-C-T		not specified	Uncertain significance (Jan 03, 2025)
11-65171415-G-T		not specified	Uncertain significance (Oct 19, 2024)
11-65171454-C-T		not specified	Uncertain significance (Dec 07, 2024)
11-65171457-T-C		not specified	Uncertain significance (Oct 26, 2022)
11-65171460-C-T		not specified	Uncertain significance (Oct 01, 2024)
11-65171490-A-G		not specified	Uncertain significance (Jan 23, 2024)
11-65171970-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-65172451-T-C		not specified	Uncertain significance (Apr 10, 2023)
11-65172469-G-A		not specified	Likely benign (Apr 01, 2024)
11-65172501-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-65172520-G-A		not specified	Likely benign (Mar 12, 2024)
11-65172573-C-T		not specified	Uncertain significance (Aug 27, 2024)
11-65172577-C-T		not specified	Uncertain significance (Jul 17, 2024)
11-65172720-C-T		not specified	Uncertain significance (Apr 26, 2023)
11-65172726-C-T		not specified	Uncertain significance (May 16, 2024)
11-65172727-G-A		not specified	Uncertain significance (Jan 20, 2023)
11-65172730-G-A		not specified	Uncertain significance (Jun 28, 2023)
11-65172748-T-G		not specified	Uncertain significance (Aug 03, 2022)
11-65172763-C-A		not specified	Uncertain significance (Dec 18, 2024)
11-65172777-C-T		not specified	Uncertain significance (Jun 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPDYC	protein_coding	protein_coding	ENST00000377185	7	3091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000487	0.877	125720	0	26	125746	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.501	160	179	0.895	0.0000108	1905
Missense in Polyphen		41	58.194	0.70454		648
Synonymous	0.990	54	64.1	0.843	0.00000346	572
Loss of Function	1.44	9	15.0	0.599	7.39e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000436	0.000434
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000388	0.0000352
Middle Eastern	0.000110	0.000109
South Asian	0.000270	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes progression through the cell cycle via binding and activation of CDK1 and CDK2. Involved in the spindle-assembly checkpoint. Required for recruitment of MAD2L1, BUBR1 and BUB1 to kinetochores. Required for the correct localization of the active form of Aurora B in prometaphase. {ECO:0000269|PubMed:15611625, ECO:0000269|PubMed:20605920}.
• Pathway: Oocyte meiosis - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.378
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.123
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.180

Gene Damage Prediction

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

Gene ontology

• Biological process: cell cycle
• Cellular component: nucleus;cytoplasm
• Molecular function: protein kinase binding