GLYR1

glyoxylate reductase 1 homolog, the group of PWWP domain containing

Basic information

Region (hg38): 16:4803203-4847288

Links

ENSG00000140632NCBI:84656OMIM:610660HGNC:24434Uniprot:Q49A26AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GLYR1 gene.

  • not_specified (50 variants)
  • GLYR1-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLYR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032569.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
51
clinvar
51
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 51 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GLYR1protein_codingprotein_codingENST00000321919 1644140
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.0002741257330141257470.0000557
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.342153360.6400.00001993627
Missense in Polyphen2068.9110.29023769
Synonymous-3.871931361.420.000009011068
Loss of Function4.94232.30.06190.00000168373

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009110.0000907
Ashkenazi Jewish0.00009990.0000992
East Asian0.00005440.0000544
Finnish0.00009370.0000924
European (Non-Finnish)0.00005290.0000527
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity (PubMed:23260659). Recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3) (PubMed:20850016). Regulates p38 MAP kinase activity by mediating stress activation of p38alpha/MAPK14 and specifically regulating MAPK14 signaling (PubMed:16352664). Indirectly promotes phosphorylation of MAPK14 and activation of ATF2 (PubMed:16352664). The phosphorylation of MAPK14 requires upstream activity of MAP2K4 and MAP2K6 (PubMed:16352664). {ECO:0000269|PubMed:16352664, ECO:0000269|PubMed:20850016, ECO:0000269|PubMed:23260659}.;

Intolerance Scores

loftool
0.108
rvis_EVS
-0.89
rvis_percentile_EVS
10.3

Haploinsufficiency Scores

pHI
hipred
Y
hipred_score
0.673
ghis
0.680

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.471

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Glyr1
Phenotype

Gene ontology

Biological process
oxidation-reduction process
Cellular component
nucleosome;nucleoplasm;Golgi apparatus;cytosol;nuclear speck
Molecular function
DNA binding;protein binding;oxidoreductase activity;methylated histone binding;histone binding;NADP binding;NAD binding