GSX1

protein-coding

GS homeobox 1, the group of HOXL subclass homeoboxes

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

GSH1

MANE transcript

NM_145657.3

Inheritance

—

ClinVar variants

U:45B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr13:27,792,483-27,794,768

External References & Databases

Ensembl (ENSG00000169840)

Transcript & Mutation Effects

hg38 • Region Span ~2.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GSX1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 46

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145657.3. 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	1
missense			45 clinvar	1 clinvar	1 clinvar	47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	1	2	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145657.3	RefSeq	NP_663632.1	2	MANE Select
ENST00000302945.3	Ensembl	ENSP00000304331.2	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spinal cord association neuron differentiation
hypothalamus development
adenohypophysis development
positive regulation of transcription by RNA polymerase II
neuron fate commitment

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
sequence-specific DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302945
Coding exons: 2
Length: 2126
Individuals with no LoFs: 122503
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 122506
p: 0.0000122

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.498	117	133	0.879	0.00000610	1646
Missense (PolyPhen)		21	41.354	0.50781		497
Synonymous	-0.597	66	60.1	1.10	0.00000288	579
Loss of Function	1.36	3	6.83	0.439	2.97e-7	79

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000091	0.0000091	rare
South Asian	0.000040	0.000034	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable transcription factor that binds to the DNA sequence 5'-GC[TA][AC]ATTA[GA]-3'. Activates the transcription of the GHRH gene. Plays an important role in pituitary development.;

Recessive Scores

pRec: 0.155

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.418

Gene Damage Prediction

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