STOX2

protein-coding

storkhead box 2

Gene summary

This gene encodes a Storkhead-box_winged-helix domain containing protein. This protein is differentially expressed in decidual tissue and may be involved in the susceptibility to pre-eclampsia with fetal growth restriction. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

MANE transcript

NM_020225.3

Inheritance

—

ClinVar variants

U:127B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr4:183,797,692-184,023,526

External References & Databases

Ensembl (ENSG00000173320)

Transcript & Mutation Effects

hg38 • Region Span ~225.8 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 STOX2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 122

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020225.3. 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			3 clinvar	1 clinvar		4
missense			122 clinvar	3 clinvar		125
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	127	4	0	131

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020225.3	RefSeq	NP_064610.1	4	MANE Select
ENST00000308497.9	Ensembl	ENSP00000311257.4	4	MANE Select
ENST00000506529.1	Ensembl	ENSP00000426209.1	2	Standard
ENST00000512520.1	Ensembl	ENSP00000425388.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

maternal placenta development
regulation of transcription by RNA polymerase II
response to bacterium
embryo development ending in birth or egg hatching

Molecular Function

molecular_function

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308497
Coding exons: 4
Length: 170096
Individuals with no LoFs: 124589
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 124627
p: 0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.33	446	532	0.838	0.0000312	6067
Missense (PolyPhen)		138	197.61	0.69834		2220
Synonymous	-0.540	232	222	1.05	0.0000145	1840
Loss of Function	3.84	6	27.8	0.216	0.00000159	348

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00045	0.00026	rare
Ashkenazi Jewish	0.00043	0.00030	rare
East Asian	0.00036	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00011	rare
South Asian	0.00026	0.00016	rare
Other	0.00072	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.147
RVIS EVS: -0.17
RVIS percentile EVS: 40.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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