GLYR1

protein-coding

glyoxylate reductase 1 homolog, the group of PWWP domain containing

Gene summary

Enables several functions, including chromatin-protein adaptor activity; histone binding activity; and nucleosome binding activity. Involved in transcription elongation-coupled chromatin remodeling and transcription initiation-coupled chromatin remodeling. Located in nucleoplasm. Part of nucleosome. Is active in chromatin. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032569.4

Inheritance

—

ClinVar variants

U:72B:1

Top phenotype

GLYR1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr16:4,803,203-4,847,288

External References & Databases

Ensembl (ENSG00000140632)

Transcript & Mutation Effects

hg38 • Region Span ~44.1 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 GLYR1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 2

GLYR1-related disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032569.4. 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		1
missense			65 clinvar			65
nonsense			1 clinvar			1
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	72	1	0	73

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032569.4	RefSeq	NP_115958.2	16	MANE Select
ENST00000321919.14	Ensembl	ENSP00000322716.6	16	MANE Select
NM_001308096.2	RefSeq	NP_001295025.1	16	Standard
NM_001324096.2	RefSeq	NP_001311025.2	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

oxidation-reduction process

Molecular Function

DNA binding
protein binding
oxidoreductase activity
methylated histone binding
histone binding

Cellular Component

nucleosome
nucleoplasm
Golgi apparatus
cytosol
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321919
Coding exons: 16
Length: 44140
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125747
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.34	215	336	0.640	0.0000199	3627
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.471

Gene Damage Prediction

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