SOX11

SRY-box transcription factor 11, the group of SRY-box transcription factors

Basic information

Region (hg38): 2:5692383-5701385

Links

ENSG00000176887 ∙ NCBI:6664 ∙ OMIM:600898 ∙ HGNC:11191 ∙ Uniprot:P35716 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal dominant 27 (Definitive), mode of inheritance: AD
• intellectual disability, autosomal dominant 27 (Definitive), mode of inheritance: AD
• intellectual disability, autosomal dominant 27 (Strong), mode of inheritance: AD
• Coffin-Siris syndrome (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism (Coffin-Siris syndrome 9)	AD	Audiologic/Otolaryngologic; Endocrine	Individuals have been described with hearling loss, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; The condition can include hypogonadotropic hypogonadism, and surveillance in adolescence related to sexual maturation, including regarding potential pharmacologic interventions, is indicated, as is monitoring of bone mineral density in order to allow early detection and treatment of disease	Audiologic/Otolaryngologic; Craniofacial; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic	24886874; 33086258; 33785884; 35341651; 35642566

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SOX11 gene.

• not provided (133 variants)
• Intellectual disability, autosomal dominant 27 (64 variants)
• Inborn genetic diseases (35 variants)
• not specified (10 variants)
• SOX11-related condition (1 variants)
• Coffin-Siris syndrome (1 variants)
• Pituitary stalk interruption syndrome (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX11 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			8	43	2	53
missense	5	33	77	9	2	126
nonsense	4	5				9
start loss						0
frameshift	2	6	1			9
inframe indel			8	1		9
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2	3	5
Total	11	44	94	55	7

Variants in SOX11

This is a list of pathogenic ClinVar variants found in the SOX11 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-5692502-C-A			Benign (Nov 27, 2018)
2-5692535-T-C			Benign (Aug 08, 2018)
2-5692574-G-C			Likely benign (Oct 07, 2019)
2-5692733-GGCGGAGAGCTTGGAA-G		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
2-5692735-C-A			Uncertain significance (Nov 18, 2023)
2-5692737-G-A			Likely benign (Jun 19, 2023)
2-5692754-G-A		SOX11-related disorder	Likely benign (Jun 20, 2023)
2-5692757-C-A		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
2-5692766-C-T			Likely benign (Dec 08, 2023)
2-5692770-G-C			Uncertain significance (Aug 20, 2023)
2-5692774-C-G		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
2-5692784-G-T			Likely benign (Jan 23, 2024)
2-5692788-G-A			Uncertain significance (Aug 30, 2023)
2-5692794-G-A			Likely benign (Nov 27, 2023)
2-5692799-C-G			Likely benign (Aug 30, 2023)
2-5692801-T-C			Uncertain significance (Dec 28, 2022)
2-5692808-C-A		Intellectual disability, autosomal dominant 27	Pathogenic (Mar 09, 2023)
2-5692816-T-G		Inborn genetic diseases	Uncertain significance (Sep 28, 2022)
2-5692832-C-A			Uncertain significance (Dec 06, 2022)
2-5692834-A-G			Uncertain significance (Jun 09, 2023)
2-5692837-C-G			Uncertain significance (Jan 12, 2024)
2-5692856-G-T			Uncertain significance (Aug 30, 2023)
2-5692859-G-C			Likely benign (Sep 28, 2022)
2-5692860-G-A		Intellectual disability, autosomal dominant 27	Uncertain significance (Mar 09, 2023)
2-5692863-C-G		Intellectual disability, autosomal dominant 27	Uncertain significance (Mar 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX11	protein_coding	protein_coding	ENST00000322002	1	8718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.858	0.141	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	146	246	0.594	0.0000114	2848
Missense in Polyphen		24	94.071	0.25513		1059
Synonymous	-2.95	153	113	1.35	0.00000577	867
Loss of Function	2.76	1	10.8	0.0927	4.63e-7	128

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: Transcriptional factor involved in the embryonic neurogenesis. May also have a role in tissue modeling during development. {ECO:0000269|PubMed:24886874}.
• Pathway: Preimplantation Embryo (Consensus)

Recessive Scores

• pRec: 0.154

Haploinsufficiency Scores

• pHI: 0.414
• hipred: Y
• hipred_score: 0.593
• ghis: 0.617

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox11
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); hematopoietic system phenotype; normal 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); respiratory system phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype

Zebrafish Information Network

• Gene name: sox11b
• Affected structure: caudal vein plexus
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;skeletal system development;kidney development;neural tube formation;lens morphogenesis in camera-type eye;outflow tract morphogenesis;cardiac ventricle formation;noradrenergic neuron differentiation;regulation of transcription, DNA-templated;translation;positive regulation of cell population proliferation;positive regulation of gene expression;negative regulation of gene expression;oligodendrocyte development;glial cell proliferation;neural crest cell development;regulation of transforming growth factor beta receptor signaling pathway;spinal cord development;glial cell development;cell differentiation;neuron differentiation;positive regulation of BMP signaling pathway;positive regulation of hippo signaling;skeletal muscle cell differentiation;positive regulation of neuron differentiation;positive regulation of osteoblast differentiation;positive regulation of ossification;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of hormone secretion;sympathetic nervous system development;embryonic digestive tract morphogenesis;embryonic skeletal system morphogenesis;negative regulation of lymphocyte proliferation;positive regulation of neurogenesis;hard palate development;soft palate development;limb bud formation;negative regulation of glial cell proliferation;ventricular septum morphogenesis;lung morphogenesis;negative regulation of cell death;neuroepithelial cell differentiation;eyelid development in camera-type eye;somite development;cornea development in camera-type eye;closure of optic fissure;signal transduction involved in cell cycle checkpoint;positive regulation of stem cell proliferation;negative regulation of transcription regulatory region DNA binding;positive regulation of lens epithelial cell proliferation
• Cellular component: nucleus;cytoplasm;nuclear transcription factor complex
• Molecular function: transcription regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;enhancer sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coactivator activity;translation factor activity, RNA binding