GLIS1

GLIS family zinc finger 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:53506237-53739164

Links

ENSG00000174332 ∙ NCBI:148979 ∙ OMIM:610378 ∙ HGNC:29525 ∙ Uniprot:Q8NBF1 ∙ 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 GLIS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLIS1 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	2	3
missense			53	1	3	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	53	2	6

Variants in GLIS1

This is a list of pathogenic ClinVar variants found in the GLIS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-53506660-G-A		not specified	Uncertain significance (Apr 04, 2024)
1-53506693-C-G		not specified	Uncertain significance (May 25, 2023)
1-53506696-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-53506740-G-A		not specified	Uncertain significance (Mar 19, 2024)
1-53509164-C-T		not specified	Uncertain significance (Aug 01, 2022)
1-53509170-G-A		not specified	Uncertain significance (Jun 16, 2023)
1-53509192-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-53509201-C-T		not specified	Uncertain significance (Feb 27, 2024)
1-53509209-C-A		not specified	Uncertain significance (Sep 12, 2023)
1-53509220-T-G		not specified	Uncertain significance (Oct 06, 2021)
1-53509256-A-T		not specified	Uncertain significance (Oct 25, 2023)
1-53509272-A-G		not specified	Uncertain significance (Oct 29, 2021)
1-53509912-G-A		not specified	Uncertain significance (Apr 12, 2024)
1-53509927-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-53509949-C-G		not specified	Uncertain significance (Feb 17, 2022)
1-53509968-G-C		not specified	Uncertain significance (Sep 16, 2021)
1-53510005-G-T		not specified	Uncertain significance (Dec 28, 2022)
1-53510013-A-G		not specified	Uncertain significance (Jun 07, 2023)
1-53510022-C-G		not specified	Uncertain significance (Dec 06, 2021)
1-53510022-C-T		not specified	Uncertain significance (Feb 13, 2023)
1-53514734-G-C		not specified	Uncertain significance (Jan 31, 2023)
1-53514751-T-C		not specified	Uncertain significance (Jun 29, 2023)
1-53514766-G-C		not specified	Uncertain significance (Sep 20, 2023)
1-53520651-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-53524767-G-C			Benign (Jun 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLIS1	protein_coding	protein_coding	ENST00000312233	8	227968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0389	0.960	125663	0	30	125693	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0422	360	362	0.994	0.0000232	3914
Missense in Polyphen		121	134.18	0.90177		1550
Synonymous	0.195	168	171	0.981	0.0000120	1333
Loss of Function	2.82	6	19.4	0.309	9.45e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000966	0.0000921
Ashkenazi Jewish	0.0000998	0.0000993
East Asian	0.000114	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000219	0.000202
Middle Eastern	0.000114	0.000109
South Asian	0.0000475	0.0000327
Other	0.000175	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as both a repressor and activator of transcription. Binds to the consensus sequence 5'-GACCACCCAC-3' (By similarity). {ECO:0000250|UniProtKB:Q8K1M4}.

Recessive Scores

• pRec: 0.0975

Intolerance Scores

• loftool: 0.136
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.29

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.694

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glis1
• Phenotype: normal phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;metal ion binding