GLYR1

glyoxylate reductase 1 homolog, the group of PWWP domain containing

Basic information

Region (hg38): 16:4803202-4847288

Links

ENSG00000140632 ∙ NCBI:84656 ∙ OMIM:610660 ∙ HGNC:24434 ∙ Uniprot:Q49A26 ∙ 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 GLYR1 gene.

• Inborn genetic diseases (9 variants)
• GLYR1-related condition (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.

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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in GLYR1

This is a list of pathogenic ClinVar variants found in the GLYR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4811187-C-A		not specified	Uncertain significance (Jan 25, 2024)
16-4811649-C-T		not specified	Uncertain significance (Sep 01, 2021)
16-4812234-C-A		not specified	Uncertain significance (Dec 11, 2023)
16-4814559-G-A		not specified	Uncertain significance (Dec 27, 2023)
16-4814563-C-A		not specified	Uncertain significance (Oct 26, 2022)
16-4821555-A-G		not specified	Uncertain significance (Jan 04, 2024)
16-4821576-T-C		not specified	Uncertain significance (May 11, 2022)
16-4822889-T-A		not specified	Uncertain significance (Feb 13, 2024)
16-4822918-G-A		not specified	Uncertain significance (Jun 01, 2022)
16-4823829-C-T		not specified	Uncertain significance (Feb 27, 2024)
16-4823849-G-A		GLYR1-related disorder	Uncertain significance (Mar 09, 2018)
16-4823850-C-T		not specified	Uncertain significance (Oct 13, 2023)
16-4823861-C-A		GLYR1-related disorder	Uncertain significance (Mar 09, 2018)
16-4823862-C-T		not specified	Uncertain significance (Oct 17, 2023)
16-4823885-C-G		not specified	Uncertain significance (Dec 19, 2023)
16-4832037-A-G		not specified	Uncertain significance (Oct 14, 2023)
16-4832094-C-T		not specified	Uncertain significance (Jun 24, 2022)
16-4832098-T-C		not specified	Uncertain significance (Dec 15, 2022)
16-4832126-G-T		not specified	Uncertain significance (May 18, 2022)
16-4832136-C-T		not specified	Uncertain significance (Jul 21, 2021)
16-4832176-T-A		not specified	Uncertain significance (Jun 29, 2022)
16-4832823-G-A		not specified	Uncertain significance (Dec 22, 2023)
16-4832896-C-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLYR1	protein_coding	protein_coding	ENST00000321919	16	44140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000274	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	215	336	0.640	0.0000199	3627
Missense in Polyphen		20	68.911	0.29023		769
Synonymous	-3.87	193	136	1.42	0.00000901	1068
Loss of Function	4.94	2	32.3	0.0619	0.00000168	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000911	0.0000907
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000937	0.0000924
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

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

• 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

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

Mouse Genome Informatics

• Gene name: Glyr1

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