ZYG11A

zyg-11 family member A, cell cycle regulator, the group of ZYG11 cell cycle regulator family|Armadillo like helical domain containing

Basic information

Region (hg38): 1:52842511-52894998

Links

ENSG00000203995 ∙ NCBI:440590 ∙ OMIM:618675 ∙ HGNC:32058 ∙ Uniprot:Q6WRX3 ∙ 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 ZYG11A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZYG11A 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			39	2	1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	1

Variants in ZYG11A

This is a list of pathogenic ClinVar variants found in the ZYG11A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52842903-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-52842914-C-G		not specified	Uncertain significance (Jun 22, 2023)
1-52842950-G-C		not specified	Uncertain significance (Jan 26, 2022)
1-52842971-C-G		not specified	Uncertain significance (Oct 03, 2023)
1-52854582-T-G		not specified	Uncertain significance (Jun 11, 2021)
1-52857112-G-A			Benign (May 17, 2018)
1-52857232-A-C		not specified	Uncertain significance (Jul 14, 2023)
1-52857286-G-C		not specified	Uncertain significance (Jun 05, 2024)
1-52857310-A-T		not specified	Uncertain significance (Feb 28, 2024)
1-52857381-A-G		not specified	Uncertain significance (Feb 28, 2024)
1-52857406-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-52857522-C-T		not specified	Uncertain significance (May 17, 2023)
1-52857525-G-T		not specified	Uncertain significance (May 02, 2024)
1-52857550-A-C		not specified	Uncertain significance (Oct 20, 2021)
1-52857669-C-T		not specified	Uncertain significance (May 16, 2024)
1-52857673-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-52857703-C-T		not specified	Uncertain significance (Oct 16, 2023)
1-52857720-G-C		not specified	Uncertain significance (Jul 09, 2021)
1-52857723-T-G		not specified	Uncertain significance (Mar 25, 2024)
1-52860827-A-G		not specified	Uncertain significance (Apr 22, 2024)
1-52860842-A-G		not specified	Uncertain significance (Dec 16, 2023)
1-52860851-A-G		not specified	Uncertain significance (Jun 17, 2024)
1-52864036-C-T		not specified	Uncertain significance (Sep 14, 2023)
1-52864050-C-G		not specified	Uncertain significance (Jun 18, 2024)
1-52864079-G-C		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZYG11A	protein_coding	protein_coding	ENST00000371528	14	52488

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-11	0.761	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	299	365	0.820	0.0000179	4992
Missense in Polyphen		71	83.267	0.85268		1223
Synonymous	1.96	107	136	0.786	0.00000664	1473
Loss of Function	1.66	22	32.2	0.684	0.00000184	393

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

• Function: FUNCTION: Probably acts as target recruitment subunit in an E3 ubiquitin ligase complex ZYGA-CUL2-elongin BC. {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.23

Haploinsufficiency Scores

• pHI: 0.119
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zyg11a

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: Cul2-RING ubiquitin ligase complex