ZYG11B

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

Basic information

Region (hg38): 1:52726453-52827336

Previous symbols: [ "ZYG11" ]

Links

ENSG00000162378 ∙ NCBI:79699 ∙ OMIM:618673 ∙ HGNC:25820 ∙ Uniprot:Q9C0D3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZYG11B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZYG11B 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			18			18
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	1	18	0	0

Variants in ZYG11B

This is a list of pathogenic ClinVar variants found in the ZYG11B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52726672-G-A		not specified	Uncertain significance (Jun 12, 2023)
1-52756485-G-A		not specified	Uncertain significance (Jan 31, 2024)
1-52756509-A-G		not specified	Uncertain significance (Sep 29, 2022)
1-52756597-G-A		not specified	Uncertain significance (Apr 22, 2024)
1-52771119-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-52771373-T-A		not specified	Uncertain significance (Sep 29, 2023)
1-52771406-A-G		not specified	Uncertain significance (Feb 10, 2023)
1-52771451-C-T		Craniofacial microsomia 1	Likely pathogenic (May 18, 2022)
1-52771532-A-C		not specified	Uncertain significance (Oct 10, 2023)
1-52771597-A-C		not specified	Uncertain significance (Apr 06, 2024)
1-52771662-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-52771680-C-A		not specified	Uncertain significance (Jun 17, 2024)
1-52779857-C-G		not specified	Uncertain significance (Jun 18, 2021)
1-52779971-A-G		not specified	Uncertain significance (Jan 24, 2023)
1-52784937-G-A		not specified	Uncertain significance (Jun 22, 2024)
1-52784989-G-A		not specified	Uncertain significance (Nov 29, 2021)
1-52801922-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-52813521-C-CT		ZYG11B-related disorder	Likely benign (Aug 03, 2022)
1-52813663-A-G		not specified	Uncertain significance (May 31, 2023)
1-52813705-G-A		not specified	Uncertain significance (Apr 20, 2024)
1-52816568-C-G		not specified	Uncertain significance (Mar 24, 2023)
1-52821509-A-C		not specified	Uncertain significance (Apr 04, 2023)
1-52821573-G-T		not specified	Uncertain significance (Aug 15, 2023)
1-52821577-G-A		not specified	Uncertain significance (Jul 19, 2022)
1-52821586-G-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZYG11B	protein_coding	protein_coding	ENST00000294353	14	100889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00164	125724	1	20	125745	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.98	176	400	0.440	0.0000207	4902
Missense in Polyphen		27	76.35	0.35363		970
Synonymous	-0.971	156	141	1.10	0.00000685	1439
Loss of Function	4.97	4	36.3	0.110	0.00000193	419

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000225	0.000210
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.0000553	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000795	0.0000703
Middle Eastern	0.0000553	0.0000544
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably acts as target recruitment subunit in the E3 ubiquitin ligase complex ZYG11B-CUL2-Elongin BC.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.362
• rvis_EVS: -1
• rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.796
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.662

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zyg11b

Gene ontology

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