OSGIN1

protein-coding

oxidative stress induced growth inhibitor 1

Gene summary

This gene encodes an oxidative stress response protein that regulates cell death. Expression of the gene is regulated by p53 and is induced by DNA damage. The protein regulates apoptosis by inducing cytochrome c release from mitochondria. It also appears to be a key regulator of both inflammatory and anti-inflammatory molecules. The loss of this protein correlates with uncontrolled cell growth and tumor formation. Naturally occurring read-through transcription exists between this gene and the neighboring upstream malonyl-CoA decarboxylase (MLYCD) gene, but the read-through transcripts are unlikely to produce a protein product. [provided by RefSeq, Aug 2011]

MANE transcript

NM_182981.3

Inheritance

—

ClinVar variants

U:83B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.96

Max pathogenic AF

—

Genomic locus

chr16:83,931,311-83,966,332

External References & Databases

Ensembl (ENSG00000140961)

Transcript & Mutation Effects

hg38 • Region Span ~35.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OSGIN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182981.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		2 clinvar	3
missense			81 clinvar	4 clinvar		85
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	83	4	2	89

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182981.3	RefSeq	NP_892026.1	5	MANE Select
ENST00000393306.6	Ensembl	ENSP00000376983.1	5	MANE Select
ENST00000361711.7	Ensembl	ENSP00000355374.3	5	Standard
ENST00000361711.8	Ensembl	ENSP00000355374.3	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development
regulation of signaling receptor activity
cell differentiation
negative regulation of cell growth
positive regulation of apoptotic process

Molecular Function

protein binding
growth factor activity

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361711
Coding exons: 5
Length: 18051
Individuals with no LoFs: 125674
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125724
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.28	378	314	1.20	0.0000204	3063
Missense (PolyPhen)		140	131.06	1.0682		1200
Synonymous	-1.11	171	154	1.11	0.0000116	1030
Loss of Function	0.140	17	17.6	0.964	0.00000102	162

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00039	0.00039	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates the differentiation and proliferation of normal cells through the regulation of cell death. {ECO:0000269|PubMed:11459809, ECO:0000269|PubMed:14570898}.;

Recessive Scores

pRec: 0.0981

Intolerance Scores

LoFtool: 0.777
RVIS EVS: -0.01
RVIS percentile EVS: 52.35

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.955

Gene Damage Prediction

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