OSR1

odd-skipped related transcription factor 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 2:19351485-19358623

Previous symbols: [ "ODD" ]

Links

ENSG00000143867 ∙ NCBI:130497 ∙ OMIM:608891 ∙ HGNC:8111 ∙ Uniprot:Q8TAX0 ∙ 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 OSR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSR1 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				4	1	5
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	16	4	2

Variants in OSR1

This is a list of pathogenic ClinVar variants found in the OSR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-19352324-G-A		not specified	Uncertain significance (Mar 11, 2022)
2-19352416-G-A			Likely benign (Aug 20, 2018)
2-19352628-T-C			Benign (Nov 12, 2018)
2-19353152-C-T			Benign (Jun 10, 2021)
2-19353237-A-C		not specified	Uncertain significance (Oct 03, 2022)
2-19353349-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-19353350-G-A			Likely benign (Sep 01, 2022)
2-19353360-G-T		not specified	Uncertain significance (Aug 04, 2023)
2-19353377-A-G			Likely benign (Jul 06, 2018)
2-19353381-G-A		not specified	Uncertain significance (Jul 12, 2023)
2-19353389-G-A			Likely benign (Sep 01, 2022)
2-19353461-C-A			Benign/Likely benign (Sep 01, 2022)
2-19353485-G-T		not specified	Uncertain significance (Apr 26, 2024)
2-19353520-T-G		not specified	Uncertain significance (Oct 12, 2021)
2-19353543-G-T		not specified	Uncertain significance (Sep 17, 2021)
2-19353597-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-19353625-C-T		not specified	Uncertain significance (Jan 04, 2022)
2-19353639-G-A		not specified	Uncertain significance (Feb 13, 2024)
2-19353679-C-T		not specified	Uncertain significance (Mar 16, 2022)
2-19353705-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-19353712-T-C		not specified	Uncertain significance (May 18, 2023)
2-19353732-T-G		not specified	Uncertain significance (Jan 24, 2024)
2-19353769-G-A		not specified	Uncertain significance (Dec 22, 2023)
2-19353777-A-G		not specified	Uncertain significance (May 14, 2024)
2-19353802-C-T		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSR1	protein_coding	protein_coding	ENST00000536433	2	7169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.863	0.135	125744	0	1	125745	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	101	164	0.618	0.00000959	1719
Missense in Polyphen		20	56.256	0.35552		599
Synonymous	0.306	73	76.4	0.955	0.00000489	570
Loss of Function	2.36	0	6.51	0.00	3.18e-7	84

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)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that plays a role in the regulation of embryonic heart and urogenital development. {ECO:0000250}.

Intolerance Scores

• loftool: 0.0916
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.387
• hipred: Y
• hipred_score: 0.604
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osr1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland 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; 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); reproductive system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; renal/urinary system phenotype; skeleton phenotype; respiratory system phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: osr1
• Affected structure: anterior lateral plate mesoderm
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;urogenital system development;ureteric bud development;mesonephros development;chondrocyte differentiation;heart development;gonad development;positive regulation of gene expression;cell differentiation;positive regulation of bone mineralization;negative regulation of epithelial cell differentiation;embryonic forelimb morphogenesis;embryonic hindlimb morphogenesis;embryonic skeletal limb joint morphogenesis;middle ear morphogenesis;odontogenesis;embryonic digit morphogenesis;negative regulation of apoptotic process;positive regulation of transcription by RNA polymerase II;intermediate mesoderm development;pronephros development;stem cell differentiation;positive regulation of epithelial cell proliferation;roof of mouth development;embryonic skeletal joint morphogenesis;cellular response to retinoic acid;metanephric mesenchyme development;cell proliferation involved in kidney development;metanephric mesenchyme morphogenesis;mesangial cell development;metanephric mesenchymal cell differentiation;posterior mesonephric tubule development;specification of anterior mesonephric tubule identity;specification of posterior mesonephric tubule identity;mesonephric duct morphogenesis;negative regulation of nephron tubule epithelial cell differentiation;renal vesicle progenitor cell differentiation;ureter urothelium development;metanephric epithelium development;metanephric smooth muscle tissue development;metanephric nephron tubule development;metanephric glomerulus vasculature development;metanephric interstitial fibroblast development;pattern specification involved in metanephros development;embryonic skeletal joint development;metanephric cap mesenchymal cell proliferation involved in metanephros development;negative regulation of creatine transmembrane transporter activity;positive regulation of gastrulation;negative regulation of sodium ion transmembrane transporter activity
• Cellular component: nucleus;cytosol;extrinsic component of membrane
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;metal ion binding