SOX12

SRY-box transcription factor 12, the group of SRY-box transcription factors

Basic information

Region (hg38): 20:325552-330224

Previous symbols: [ "SOX22" ]

Links

ENSG00000177732 ∙ NCBI:6666 ∙ OMIM:601947 ∙ HGNC:11198 ∙ Uniprot:O15370 ∙ 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 SOX12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX12 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					2	2
missense			34		1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	3

Variants in SOX12

This is a list of pathogenic ClinVar variants found in the SOX12 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-325962-G-A		not specified	Uncertain significance (Oct 20, 2024)
20-325967-C-T		not specified	Uncertain significance (Jun 17, 2022)
20-325971-C-T		not specified	Uncertain significance (Jan 03, 2024)
20-325973-C-A		not specified	Uncertain significance (Feb 15, 2025)
20-325991-G-A		not specified	Uncertain significance (Aug 12, 2021)
20-326117-A-C		not specified	Uncertain significance (Dec 24, 2024)
20-326173-C-G		not specified	Uncertain significance (Jul 27, 2024)
20-326271-A-T		not specified	Uncertain significance (Oct 12, 2021)
20-326276-G-T		not specified	Uncertain significance (Oct 14, 2021)
20-326277-C-A		not specified	Uncertain significance (Jul 05, 2023)
20-326306-G-T		not specified	Uncertain significance (Feb 07, 2025)
20-326342-C-T		not specified	Uncertain significance (May 16, 2024)
20-326355-G-C		not specified	Uncertain significance (Jul 16, 2024)
20-326357-C-T		not specified	Uncertain significance (Sep 06, 2022)
20-326390-G-A		not specified	Uncertain significance (Dec 02, 2024)
20-326402-G-A		not specified	Uncertain significance (May 16, 2024)
20-326414-G-T		not specified	Uncertain significance (Jun 06, 2023)
20-326454-G-T		not specified	Uncertain significance (Sep 02, 2024)
20-326475-G-C		not specified	Uncertain significance (Dec 05, 2022)
20-326499-C-A		not specified	Uncertain significance (Dec 07, 2021)
20-326523-C-G		not specified	Uncertain significance (Jan 20, 2023)
20-326528-C-G		not specified	Uncertain significance (Feb 07, 2023)
20-326535-A-G		not specified	Uncertain significance (Apr 13, 2022)
20-326538-G-A		not specified	Uncertain significance (Jan 10, 2025)
20-326546-G-C		not specified	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX12	protein_coding	protein_coding	ENST00000342665	1	4659

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.856	0.142	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	78	137	0.570	0.00000637	1975
Missense in Polyphen		8	28.294	0.28275		328
Synonymous	0.417	59	63.2	0.933	0.00000306	671
Loss of Function	2.34	0	6.35	0.00	2.74e-7	94

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: Binds to the sequence 5'-AACAAT-3'. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.287

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.441

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox12
• Phenotype: craniofacial 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); limbs/digits/tail 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); normal phenotype; embryo phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;spinal cord development;cell differentiation;cell fate commitment;positive regulation of transcription by RNA polymerase II;protein-DNA complex assembly
• Cellular component: cellular_component;nucleus;nucleoplasm;protein-DNA complex;nuclear transcription factor complex
• Molecular function: transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;transcription coactivator activity