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.

not_specified (81 variants)
not_provided (6 variants)
SOX7-related_disorder (4 variants)

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. These statistics are base on transcript: NM_000031439.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	3 clinvar	7
missense			79 clinvar	1 clinvar	1 clinvar	81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	5	4

Loading clinvar variants...

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