SOX17

SRY-box transcription factor 17, the group of SRY-box transcription factors

Basic information

Region (hg38): 8:54457934-54460892

Links

ENSG00000164736 ∙ NCBI:64321 ∙ OMIM:610928 ∙ HGNC:18122 ∙ Uniprot:Q9H6I2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• vesicoureteral reflux 3 (Definitive), mode of inheritance: AD
• familial vesicoureteral reflux (Supportive), mode of inheritance: AD
• vesicoureteral reflux 3 (Strong), mode of inheritance: AD
• vesicoureteral reflux 3 (Limited), mode of inheritance: AD
• pulmonary arterial hypertension (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Vesicoureteral reflux 3	AD	Renal	Monitoring and intervention related to vesicoureteral reflux may be beneficial in terms of helping to preserve renal function	Renal	20960469

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SOX17 gene.

• not provided (76 variants)
• Inborn genetic diseases (21 variants)
• Vesicoureteral reflux 3 (8 variants)
• SOX17-related condition (2 variants)
• not specified (1 variants)
• Vesicoureteral reflux (1 variants)
• Chronic kidney disease (1 variants)
• Pulmonary arterial hypertension (1 variants)
• Sox17- related disorders (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX17 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	19	5	25
missense		3	48	6	4	61
nonsense	1					1
start loss						0
frameshift	1					1
inframe indel			2		1	3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	7	10
Total	2	3	51	28	17

Highest pathogenic variant AF is 0.00000657

Variants in SOX17

This is a list of pathogenic ClinVar variants found in the SOX17 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-54458059-C-T			Benign (Nov 12, 2018)
8-54458189-G-T		SOX17-related disorder	Uncertain significance (Sep 16, 2022)
8-54458195-G-C			Likely benign (Jul 30, 2021)
8-54458195-G-T			Likely benign (Jul 25, 2022)
8-54458196-C-G		Inborn genetic diseases	Uncertain significance (Nov 07, 2023)
8-54458236-C-A			Benign (Dec 18, 2023)
8-54458255-C-T			Likely benign (Sep 15, 2023)
8-54458302-C-T			Uncertain significance (May 17, 2022)
8-54458305-C-A		Inborn genetic diseases	Uncertain significance (Aug 28, 2023)
8-54458308-G-A		Inborn genetic diseases	Uncertain significance (Sep 27, 2022)
8-54458330-C-T			Uncertain significance (Apr 20, 2021)
8-54458346-C-G		Sox17- related disorders	Likely pathogenic (-)
8-54458352-A-T		Inborn genetic diseases	Uncertain significance (Mar 02, 2022)
8-54458359-C-T			Uncertain significance (Dec 21, 2023)
8-54458379-G-A		Inborn genetic diseases	Uncertain significance (Aug 30, 2022)
8-54458381-C-G			Uncertain significance (Dec 24, 2021)
8-54458383-A-G		Vesicoureteral reflux 3	Likely pathogenic (Jul 18, 2022)
8-54458386-G-A			Uncertain significance (Sep 27, 2022)
8-54458411-A-T		SOX17-related disorder	Benign (Jan 25, 2024)
8-54458422-A-G			Uncertain significance (May 12, 2021)
8-54458456-G-C			Likely benign (Jun 01, 2022)
8-54458465-C-A			Likely benign (Jul 03, 2023)
8-54458520-C-CAG			Benign (Nov 12, 2018)
8-54458594-C-T			Benign (Nov 12, 2018)
8-54458912-C-A			Benign (May 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX17	protein_coding	protein_coding	ENST00000297316	2	2954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.885	0.115	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.774	199	232	0.857	0.0000107	2618
Missense in Polyphen		86	110.83	0.776		1264
Synonymous	-1.36	122	104	1.17	0.00000521	855
Loss of Function	2.86	1	11.4	0.0876	5.00e-7	118

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as transcription regulator that binds target promoter DNA and bends the DNA. Binds to the sequences 5'- AACAAT-'3 or 5'-AACAAAG-3'. Modulates transcriptional regulation via WNT3A. Inhibits Wnt signaling. Promotes degradation of activated CTNNB1. Plays a key role in the regulation of embryonic development. Required for normal looping of the embryonic heart tube. Required for normal development of the definitive gut endoderm. Probable transcriptional activator in the premeiotic germ cells (By similarity). {ECO:0000250}.
• Pathway: Wnt signaling pathway - Homo sapiens (human);Cardiac Progenitor Differentiation;Endoderm Differentiation;Mesodermal Commitment Pathway;Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;Deactivation of the beta-catenin transactivating complex;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.226

Haploinsufficiency Scores

• pHI: 0.102
• hipred: Y
• hipred_score: 0.837
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.726

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox17
• Phenotype: immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; liver/biliary system phenotype; embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: sox17
• Affected structure: erythroid lineage cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;angiogenesis;vasculogenesis;endoderm formation;inner cell mass cellular morphogenesis;heart looping;cardiogenic plate morphogenesis;embryonic heart tube morphogenesis;outflow tract morphogenesis;negative regulation of Wnt signaling pathway involved in heart development;regulation of transcription, DNA-templated;spermatogenesis;endodermal cell fate determination;rostrocaudal neural tube patterning;signal transduction involved in regulation of gene expression;cell differentiation;negative regulation of cell growth;protein destabilization;embryonic heart tube development;cell migration involved in gastrulation;negative regulation of mesodermal cell fate specification;mRNA transcription by RNA polymerase II;positive regulation of cell differentiation;positive regulation of protein catabolic process;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;regulation of embryonic development;embryonic foregut morphogenesis;positive regulation of skeletal muscle tissue development;stem cell fate specification;protein stabilization;canonical Wnt signaling pathway;endocardium formation;regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification;cardiac cell fate determination;heart formation;endocardial cell differentiation;common bile duct development;gall bladder development;endodermal digestive tract morphogenesis;renal system development;regulation of stem cell proliferation;negative regulation of canonical Wnt signaling pathway;cellular response to leukemia inhibitory factor;regulation of stem cell division;regulation of cardiac cell fate specification
• Cellular component: nucleus;nucleoplasm;transcription factor complex;nuclear transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;transcription coactivator activity;protein binding;beta-catenin binding;transcription factor binding;sequence-specific DNA binding;transcription regulatory region DNA binding;protein heterodimerization activity