GON4L

gon-4 like, the group of Myb/SANT domain containing

Basic information

Region (hg38): 1:155749659-155859400

Previous symbols: [ "GON4" ]

Links

ENSG00000116580 ∙ NCBI:54856 ∙ OMIM:610393 ∙ HGNC:25973 ∙ Uniprot:Q3T8J9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GON4L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GON4L 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				1		1
missense			1	2		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	3	0

Variants in GON4L

This is a list of pathogenic ClinVar variants found in the GON4L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155751759-G-A		GON4L-related disorder	Likely benign (Jul 18, 2019)
1-155752148-A-G		GON4L-related disorder	Likely benign (May 19, 2021)
1-155752183-G-T			Likely benign (Feb 01, 2023)
1-155752298-C-T		GON4L-related disorder	Likely benign (Jul 29, 2019)
1-155752301-G-A		GON4L-related disorder	Likely benign (Sep 08, 2021)
1-155752391-C-T		GON4L-related disorder	Likely benign (Nov 01, 2022)
1-155753213-G-T			Uncertain significance (Oct 24, 2017)
1-155756957-C-T		LI-TAKADA-MIYAKE SYNDROME	Pathogenic (May 23, 2025)
1-155762384-C-G		GON4L-related disorder	Benign (Aug 06, 2019)
1-155763394-T-C		GON4L-related disorder	Likely benign (Feb 22, 2019)
1-155763466-T-G		GON4L-related disorder	Likely benign (Jul 15, 2019)
1-155763567-G-A		GON4L-related disorder	Likely benign (Aug 23, 2019)
1-155765357-C-T		GON4L-related disorder	Likely benign (Mar 03, 2020)
1-155765930-A-G		GON4L-related disorder	Likely benign (Apr 29, 2019)
1-155765999-G-A		GON4L-related disorder	Benign (Mar 07, 2019)
1-155766096-T-G		GON4L-related disorder	Likely benign (Jun 25, 2019)
1-155766197-G-C		GON4L-related disorder	Likely benign (Apr 05, 2019)
1-155766250-C-T		GON4L-related disorder	Likely benign (Jul 06, 2022)
1-155766467-C-T		GON4L-related disorder	Likely benign (Mar 05, 2019)
1-155771214-C-T		GON4L-related disorder	Likely benign (Jan 20, 2020)
1-155773106-T-C		Ependymoma	Uncertain significance (Dec 29, 2017)
1-155776454-G-C		GON4L-related disorder	Likely benign (Jan 01, 2024)
1-155777673-A-G		GON4L-related disorder	Likely benign (Dec 06, 2019)
1-155805082-A-G		GON4L-related disorder	Likely benign (Apr 12, 2019)
1-155813739-C-T		GON4L-related disorder	Likely benign (Dec 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GON4L	protein_coding	protein_coding	ENST00000437809	31	109684

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.952	0.0485	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	984	1.14e+3	0.863	0.0000606	14719
Missense in Polyphen		278	335.93	0.82755		4402
Synonymous	-0.513	435	422	1.03	0.0000217	4368
Loss of Function	7.13	19	93.3	0.204	0.00000501	1222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000232	0.000232
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.000109	0.000109
Finnish	0.000236	0.000231
European (Non-Finnish)	0.000159	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000163
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has transcriptional repressor activity, probably as part of a complex with YY1, SIN3A AND HDAC1. Required for B cell lymphopoiesis. {ECO:0000250|UniProtKB:Q9DB00}.

Recessive Scores

• pRec: 0.0872

Intolerance Scores

• loftool: 0.572
• rvis_EVS: -1.36
• rvis_percentile_EVS: 4.54

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.466
• ghis: 0.605

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.237

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gon4l
• Phenotype: neoplasm; hematopoietic system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: gon4l
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: immature

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;B cell differentiation;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;transcription corepressor activity