SOX7

SRY-box transcription factor 7, the group of SRY-box transcription factors

Basic information

Region (hg38): 8:10723768-10730511

Links

ENSG00000171056 ∙ NCBI:83595 ∙ OMIM:612202 ∙ HGNC:18196 ∙ Uniprot:Q9BT81 ∙ 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 SOX7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX7 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	3	4
missense			47		1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	1	4

Variants in SOX7

This is a list of pathogenic ClinVar variants found in the SOX7 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-10725782-C-A		not specified	Uncertain significance (Sep 27, 2024)
8-10725820-G-T		not specified	Uncertain significance (Sep 16, 2021)
8-10725842-C-T		not specified	Uncertain significance (Oct 20, 2024)
8-10725844-T-C		not specified	Uncertain significance (Aug 07, 2024)
8-10725860-T-A		not specified	Uncertain significance (Feb 14, 2025)
8-10725860-T-C		not specified	Likely benign (Feb 25, 2025)
8-10725883-T-A		not specified	Uncertain significance (Nov 21, 2023)
8-10725886-C-T		not specified	Uncertain significance (Apr 27, 2022)
8-10725887-C-G		not specified	Uncertain significance (Jul 31, 2024)
8-10725916-T-C		not specified	Uncertain significance (Aug 03, 2022)
8-10725929-C-T		not specified	Uncertain significance (Feb 28, 2023)
8-10725940-T-C		not specified	Uncertain significance (Sep 16, 2021)
8-10725944-C-T		not specified	Uncertain significance (Nov 13, 2024)
8-10725966-G-A			Benign (Dec 31, 2019)
8-10726035-G-T		not specified	Uncertain significance (May 08, 2023)
8-10726048-G-A		not specified	Uncertain significance (Feb 08, 2025)
8-10726070-G-C		not specified	Uncertain significance (May 09, 2023)
8-10726076-AGCCGGGTACAGGGGACATCATGGAGAC-A		SOX7-related disorder	Likely benign (Jun 16, 2022)
8-10726088-G-A		not specified	Uncertain significance (Oct 16, 2023)
8-10726092-C-T		not specified	Uncertain significance (Oct 08, 2024)
8-10726104-G-T		SOX7-related disorder	Likely benign (Sep 01, 2022)
8-10726106-C-T			Benign (May 15, 2018)
8-10726109-G-C		not specified	Uncertain significance (Mar 17, 2023)
8-10726113-C-G		not specified	Uncertain significance (Nov 06, 2015)
8-10726144-C-T		not specified	Uncertain significance (Aug 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX7	protein_coding	protein_coding	ENST00000304501	2	116080

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.479	0.516	125733	0	9	125742	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.744	289	256	1.13	0.0000165	2449
Missense in Polyphen		83	88.422	0.93868		882
Synonymous	-2.29	156	124	1.26	0.00000889	836
Loss of Function	2.37	2	10.2	0.197	4.33e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000901	0.0000901
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000196	0.0000176
Middle Eastern	0.000110	0.000109
South Asian	0.0000694	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to and activates the CDH5 promoter, hence plays a role in the transcriptional regulation of genes expressed in the hemogenic endothelium and blocks further differentiation into blood precursors (By similarity). May be required for the survival of both hematopoietic and endothelial precursors during specification (By similarity). Competes with GATA4 for binding and activation of the FGF3 promoter (By similarity). Represses Wnt/beta-catenin-stimulated transcription, probably by targeting CTNNB1 to proteasomal degradation. Binds the DNA sequence 5'- AACAAT-3'. {ECO:0000250, ECO:0000269|PubMed:18819930}.
• Pathway: Endoderm Differentiation;Signaling by WNT;Signal Transduction;Deactivation of the beta-catenin transactivating complex;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.0872
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.378
• hipred: Y
• hipred_score: 0.502
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox7
• Phenotype: 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); 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); embryo phenotype; liver/biliary system phenotype; muscle phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: sox7
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;endoderm formation;regulation of transcription, DNA-templated;negative regulation of cell population proliferation;cell differentiation;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;regulation of canonical Wnt signaling pathway
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;transcription regulatory region DNA binding