GLRX3

glutaredoxin 3, the group of Glutaredoxin domain containing

Basic information

Region (hg38): 10:130136390-130184521

Previous symbols: [ "TXNL2" ]

Links

ENSG00000108010 ∙ NCBI:10539 ∙ OMIM:612754 ∙ HGNC:15987 ∙ Uniprot:O76003 ∙ 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 GLRX3 gene.

• Inborn genetic diseases (13 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLRX3 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in GLRX3

This is a list of pathogenic ClinVar variants found in the GLRX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-130136425-C-T		not specified	Uncertain significance (Jan 12, 2024)
10-130136430-G-A		not specified	Uncertain significance (Dec 19, 2023)
10-130136451-G-A		not specified	Uncertain significance (Oct 12, 2021)
10-130136473-C-T		not specified	Uncertain significance (Jun 01, 2023)
10-130145239-C-T		not specified	Uncertain significance (Mar 27, 2023)
10-130145269-G-A		not specified	Uncertain significance (Jan 30, 2024)
10-130160871-A-G		not specified	Uncertain significance (Oct 27, 2022)
10-130160872-G-A		not specified	Uncertain significance (Mar 20, 2023)
10-130160914-A-T		not specified	Uncertain significance (May 17, 2023)
10-130160926-G-A		not specified	Uncertain significance (Jul 06, 2022)
10-130160947-C-G		not specified	Uncertain significance (Jun 21, 2023)
10-130160961-C-G		not specified	Uncertain significance (Mar 31, 2022)
10-130166513-G-A		not specified	Uncertain significance (Sep 01, 2021)
10-130166520-G-A			Benign (Dec 31, 2019)
10-130166543-A-G		not specified	Uncertain significance (Apr 18, 2023)
10-130169440-G-T		not specified	Uncertain significance (Dec 15, 2023)
10-130175000-C-T		not specified	Uncertain significance (Oct 05, 2021)
10-130175033-A-T		not specified	Uncertain significance (Oct 05, 2023)
10-130179361-A-C		not specified	Uncertain significance (Sep 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLRX3	protein_coding	protein_coding	ENST00000368644	11	48123

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.358	0.642	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.148	157	162	0.967	0.00000790	2173
Missense in Polyphen		39	51.808	0.75278		670
Synonymous	0.728	50	57.0	0.877	0.00000279	627
Loss of Function	3.36	5	22.0	0.227	0.00000117	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Together with BOLA2, acts as a cytosolic iron-sulfur (Fe-S) cluster assembly factor that facilitates [2Fe-2S] cluster insertion into a subset of cytosolic proteins (PubMed:26613676, PubMed:27519415). Acts as a critical negative regulator of cardiac hypertrophy and a positive inotropic regulator (By similarity). Required for hemoglobin maturation (PubMed:23615448). Does not possess any thyoredoxin activity since it lacks the conserved motif that is essential for catalytic activity. {ECO:0000250|UniProtKB:Q9CQM9, ECO:0000269|PubMed:23615448, ECO:0000269|PubMed:26613676, ECO:0000269|PubMed:27519415}.
• Pathway: Transport of small molecules;Iron uptake and transport (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.704
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.472
• hipred: Y
• hipred_score: 0.739
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.673

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glrx3
• 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); 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); 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); embryo phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: glrx3
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of the force of heart contraction;cellular iron ion homeostasis;negative regulation of cardiac muscle hypertrophy;electron transport chain;[2Fe-2S] cluster assembly;cell redox homeostasis;protein maturation by iron-sulfur cluster transfer
• Cellular component: nucleus;cytosol;cell cortex;Z disc;dendrite
• Molecular function: RNA binding;protein kinase C binding;protein binding;electron transfer activity;protein disulfide oxidoreductase activity;glutathione disulfide oxidoreductase activity;identical protein binding;metal ion binding;iron-sulfur cluster binding