SOBP

sine oculis binding protein homolog

Basic information

Region (hg38): 6:107490105-107661306

Links

ENSG00000112320 ∙ NCBI:55084 ∙ OMIM:613667 ∙ HGNC:29256 ∙ Uniprot:A7XYQ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, anterior maxillary protrusion, and strabismus (Limited), mode of inheritance: AR
• intellectual disability, anterior maxillary protrusion, and strabismus (Supportive), mode of inheritance: AR
• intellectual disability, anterior maxillary protrusion, and strabismus (Limited), mode of inheritance: Unknown
• syndromic intellectual disability (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Impaired intellectual development, anterior maxillary protrusion, and strabismus	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	17618476; 21035105

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOBP 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			6	29	1	36
missense			63	4	2	69
nonsense						0
start loss						0
frameshift						0
inframe indel			1	4		5
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	0	0	71	37	3

Variants in SOBP

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

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

Position	Type	Phenotype	Significance	ClinVar
6-107490640-G-C			Likely benign (Jul 06, 2018)
6-107490648-C-A		not specified	Uncertain significance (Feb 06, 2024)
6-107490654-A-G			Likely benign (Dec 31, 2019)
6-107490661-G-C			Likely benign (Nov 01, 2022)
6-107490663-G-A			Uncertain significance (Apr 01, 2022)
6-107503756-A-G		not specified	Uncertain significance (Jun 07, 2024)
6-107503779-C-T		not specified	Conflicting classifications of pathogenicity (Mar 29, 2018)
6-107506248-C-G		not specified	Uncertain significance (Nov 03, 2023)
6-107506271-G-A		not specified	Uncertain significance (May 09, 2023)
6-107506288-A-G			Likely benign (Nov 15, 2017)
6-107506325-A-G		not specified	Benign/Likely benign (Dec 31, 2019)
6-107506405-A-G			Likely benign (Jul 31, 2018)
6-107506419-C-T		not specified	Uncertain significance (Mar 02, 2016)
6-107506420-A-G		not specified	Uncertain significance (Sep 28, 2017)
6-107506421-C-T		Intellectual disability, anterior maxillary protrusion, and strabismus • not specified	Uncertain significance (Dec 11, 2023)
6-107506422-C-A		not specified	Uncertain significance (Jan 23, 2024)
6-107533481-A-C		not specified	Uncertain significance (Aug 13, 2021)
6-107533495-G-C		not specified	Uncertain significance (Sep 17, 2021)
6-107533563-G-A		not specified	Uncertain significance (May 05, 2023)
6-107533576-C-T		not specified	Uncertain significance (Jul 06, 2022)
6-107533622-G-A		not specified	Uncertain significance (Jun 12, 2013)
6-107587077-C-T		Intellectual disability, anterior maxillary protrusion, and strabismus	Uncertain significance (Feb 26, 2018)
6-107587128-G-A		Intellectual disability, anterior maxillary protrusion, and strabismus • not specified	Uncertain significance (Nov 27, 2023)
6-107587137-A-G		not specified	Uncertain significance (Oct 12, 2022)
6-107587145-G-T		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOBP	protein_coding	protein_coding	ENST00000317357	6	170196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000281	124692	0	5	124697	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	365	484	0.754	0.0000307	5616
Missense in Polyphen		145	233.22	0.62173		2577
Synonymous	0.616	215	227	0.948	0.0000176	1833
Loss of Function	4.48	0	23.4	0.00	0.00000130	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.0000557	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Implicated in development of the cochlea. {ECO:0000250|UniProtKB:Q0P5V2}.
• Disease: DISEASE: Mental retardation, anterior maxillary protrusion, and strabismus (MRAMS) [MIM:613671]: A syndrome characterized by severe mental retardation, strabismus and dysmorphic features such as anterior maxillary protrusion with vertical maxillary excess, open bite and prominent crowded teeth. Some patients may lack dysmorphic features and manifest temporal lobe epilepsy and psychosis. Esotropia and amblyopia are present in some individuals. {ECO:0000269|PubMed:21035105}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.0220
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.156
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.578

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sobp
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: sensory perception of sound;locomotory behavior;inner ear morphogenesis;cognition;cochlea development
• Cellular component: nucleus
• Molecular function: SUMO polymer binding;metal ion binding