GLI4

GLI family zinc finger 4, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 8:143267433-143276931

Links

ENSG00000250571 ∙ NCBI:2738 ∙ OMIM:165280 ∙ HGNC:4320 ∙ Uniprot:P10075 ∙ 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 GLI4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLI4 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			51	1		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	1	0

Variants in GLI4

This is a list of pathogenic ClinVar variants found in the GLI4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-143269401-C-T		not specified	Uncertain significance (Nov 07, 2022)
8-143269417-T-G		not specified	Uncertain significance (Dec 05, 2024)
8-143269483-C-G		not specified	Uncertain significance (Oct 04, 2022)
8-143269486-C-G		not specified	Uncertain significance (Jan 08, 2024)
8-143274766-G-C		not specified	Uncertain significance (Mar 01, 2023)
8-143274781-G-A		not specified	Uncertain significance (Jan 31, 2025)
8-143275911-C-G		not specified	Uncertain significance (Feb 06, 2024)
8-143275915-A-C		not specified	Uncertain significance (Jan 23, 2024)
8-143275917-C-A		not specified	Uncertain significance (Feb 04, 2025)
8-143275927-G-T		not specified	Uncertain significance (Oct 16, 2024)
8-143275930-C-T		not specified	Uncertain significance (Dec 11, 2023)
8-143275935-G-A		not specified	Uncertain significance (Jul 27, 2024)
8-143275948-C-T		not specified	Uncertain significance (Sep 27, 2021)
8-143275965-G-A		not specified	Uncertain significance (Jun 24, 2022)
8-143275980-C-T		not specified	Uncertain significance (Feb 15, 2023)
8-143275998-C-T		not specified	Uncertain significance (Nov 17, 2023)
8-143275999-G-A		not specified	Uncertain significance (Aug 09, 2021)
8-143275999-G-T		not specified	Uncertain significance (Dec 28, 2023)
8-143276001-A-G		not specified	Uncertain significance (Jun 17, 2024)
8-143276053-C-T		not specified	Uncertain significance (Oct 11, 2024)
8-143276073-G-A		not specified	Uncertain significance (Jan 25, 2023)
8-143276080-G-T		not specified	Uncertain significance (Sep 24, 2024)
8-143276115-G-A		not specified	Uncertain significance (Oct 08, 2024)
8-143276128-C-T		not specified	Uncertain significance (Oct 03, 2022)
8-143276136-C-A		not specified	Likely benign (May 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLI4	protein_coding	protein_coding	ENST00000340042	3	9499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00237	0.933	125649	0	19	125668	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.679	238	210	1.13	0.0000126	2397
Missense in Polyphen		115	96.482	1.1919		1011
Synonymous	-1.02	112	99.1	1.13	0.00000675	763
Loss of Function	1.61	6	12.0	0.499	5.20e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000583	0.0000583
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000616
Middle Eastern	0.00	0.00
South Asian	0.000328	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Tumor suppressor activity of SMARCB1 (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.238
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;biological_process
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA binding;DNA-binding transcription factor activity;metal ion binding