OSR2

odd-skipped related transciption factor 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 8:98944403-98952104

Links

ENSG00000164920 ∙ NCBI:116039 ∙ OMIM:611297 ∙ HGNC:15830 ∙ Uniprot:Q8N2R0 ∙ 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 OSR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSR2 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		1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	1	1

Variants in OSR2

This is a list of pathogenic ClinVar variants found in the OSR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-98948934-A-C			Benign (Jun 19, 2018)
8-98949091-C-G		not specified	Uncertain significance (Feb 05, 2024)
8-98949197-G-A		not specified	Uncertain significance (Jan 26, 2022)
8-98949209-C-A		not specified	Uncertain significance (May 31, 2022)
8-98949265-G-A		not specified	Uncertain significance (Feb 06, 2024)
8-98949281-A-G		not specified	Uncertain significance (Oct 02, 2023)
8-98949342-G-C			Likely benign (Jun 19, 2018)
8-98949356-A-G		not specified	Uncertain significance (Oct 27, 2021)
8-98949427-C-T		not specified	Uncertain significance (Feb 14, 2024)
8-98951616-G-A		not specified	Uncertain significance (Mar 30, 2024)
8-98951620-C-T		not specified	Likely benign (Mar 30, 2024)
8-98951625-A-G		not specified	Uncertain significance (Mar 30, 2024)
8-98951659-G-A		not specified	Likely benign (Mar 30, 2024)
8-98951664-G-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSR2	protein_coding	protein_coding	ENST00000297565	3	7702

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.130	0.850	124591	0	3	124594	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	115	185	0.621	0.00000934	2054
Missense in Polyphen		13	41.017	0.31694		476
Synonymous	-0.563	88	81.5	1.08	0.00000439	628
Loss of Function	2.01	3	9.77	0.307	4.59e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000510	0.0000464
European (Non-Finnish)	0.00000886	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.477
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.588
• hipred: Y
• hipred_score: 0.693
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osr2
• Phenotype: craniofacial phenotype; growth/size/body region 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); vision/eye phenotype; digestive/alimentary phenotype; hearing/vestibular/ear phenotype; skeleton phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: osr2
• Affected structure: pectoral fin
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;urogenital system development;metanephros development;mesonephros development;chondrocyte differentiation;positive regulation of cell population proliferation;embryo development ending in birth or egg hatching;positive regulation of gene expression;cell differentiation;positive regulation of bone mineralization;osteoblast proliferation;embryonic forelimb morphogenesis;embryonic hindlimb morphogenesis;embryonic skeletal limb joint morphogenesis;middle ear morphogenesis;odontogenesis;embryonic digit morphogenesis;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;positive regulation of epithelial cell proliferation;roof of mouth development;embryonic skeletal joint morphogenesis;head development;bone morphogenesis;eyelid development in camera-type eye;embryonic skeletal joint development
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding;metal ion binding