GLIS1

protein-coding

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

Gene summary

GLIS1 is a GLI (MIM 165220)-related Kruppel-like zinc finger protein that functions as an activator and repressor of transcription (Kim et al., 2002 [PubMed 12042312]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001367484.1

Inheritance

ClinVar variants

U:117B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr1:53,506,237-53,739,164

External References & Databases

Ensembl (ENSG00000174332)

Transcript & Mutation Effects

hg38 • Region Span ~232.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

glaucomaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0005041

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GLIS1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 115

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001367484.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar	2 clinvar	5
missense			115 clinvar	3 clinvar	3 clinvar	121
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	117	5	5	127

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001367484.1	RefSeq	NP_001354413.1	10	MANE Select
ENST00000628545.2	Ensembl	ENSP00000486112.1	10	MANE Select
NM_001390836.1	RefSeq	NP_001377765.1	11	Standard
NM_001390837.1	RefSeq	NP_001377766.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
positive regulation of transcription by RNA polymerase II

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000312233
Coding exons: 8
Length: 227968
Individuals with no LoFs: 125663
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125693
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0422	360	362	0.994	0.0000232	3914
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000062	rare
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00020	rare
South Asian	0.000047	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.654

Gene Damage Prediction

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