GLYR1

Summary

GLYR1 (glyoxylate reductase 1 homolog, HGNC:24434) is a protein-coding gene on chromosome 16p13.3, encoding Cytokine-like nuclear factor N-PAC (Q49A26). Cytokine-like nuclear factor with chromatin gene reader activity involved in chromatin modification and regulation of gene expression.

Enables several functions, including chromatin-protein adaptor activity; methylated histone binding activity; and nucleosome binding activity. Involved in transcription elongation-coupled chromatin remodeling and transcription initiation-coupled chromatin remodeling. Located in cytosol and nucleoplasm. Part of nucleosome. Is active in chromatin.

Source: NCBI Gene 84656 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 87 total
• MANE Select transcript: NM_032569

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24434
Approved symbol	GLYR1
Name	glyoxylate reductase 1 homolog
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	BM045, HIBDL, NP60, N-PAC
Ensembl gene	ENSG00000140632
Ensembl biotype	protein_coding
OMIM	610660
Entrez	84656

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 22 protein_coding, 4 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000321919, ENST00000436648, ENST00000586095, ENST00000586901, ENST00000587297, ENST00000587875, ENST00000587936, ENST00000588297, ENST00000588732, ENST00000589389, ENST00000591159, ENST00000591451, ENST00000591846, ENST00000899194, ENST00000899195, ENST00000899196, ENST00000899197, ENST00000899198, ENST00000899199, ENST00000899200, ENST00000899201, ENST00000925081, ENST00000925082, ENST00000925083, ENST00000925084, ENST00000925085, ENST00000925086, ENST00000925087, ENST00000925088

RefSeq mRNA: 5 — MANE Select: NM_032569 NM_001308096, NM_001324096, NM_001324097, NM_001324098, NM_032569

CCDS: CCDS10524, CCDS81945, CCDS92098

Canonical transcript exons

ENST00000321919 — 16 exons

Exon	Start	End
ENSE00002618962	4847228	4847288
ENSE00002964292	4803203	4805310
ENSE00003484556	4832774	4832912
ENSE00003496270	4813737	4813838
ENSE00003498523	4821380	4821453
ENSE00003507242	4822875	4822931
ENSE00003530738	4821547	4821597
ENSE00003531780	4823821	4823907
ENSE00003541496	4831979	4832221
ENSE00003549941	4812086	4812248
ENSE00003572263	4845074	4845153
ENSE00003585011	4817598	4817697
ENSE00003640006	4814537	4814647
ENSE00003649255	4846174	4846210
ENSE00003669348	4811623	4811802
ENSE00003694236	4811170	4811294

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 97.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.2610 / max 717.6807, expressed in 1820 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156131	42.9190	1820
156130	0.3420	136

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	97.44	gold quality
mononuclear cell	CL:0000842	97.34	gold quality
leukocyte	CL:0000738	97.05	gold quality
right uterine tube	UBERON:0001302	96.99	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.99	gold quality
lower esophagus	UBERON:0013473	95.98	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.69	gold quality
rectum	UBERON:0001052	95.68	gold quality
mucosa of stomach	UBERON:0001199	95.47	gold quality
cerebellar hemisphere	UBERON:0002245	95.38	gold quality
cerebellar cortex	UBERON:0002129	95.31	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.28	gold quality
adenohypophysis	UBERON:0002196	95.21	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.21	gold quality
islet of Langerhans	UBERON:0000006	95.11	gold quality
transverse colon	UBERON:0001157	95.10	gold quality
metanephros cortex	UBERON:0010533	94.91	gold quality
body of stomach	UBERON:0001161	94.80	gold quality
prefrontal cortex	UBERON:0000451	94.76	gold quality
right lobe of thyroid gland	UBERON:0001119	94.74	gold quality
cerebellum	UBERON:0002037	94.73	gold quality
pituitary gland	UBERON:0000007	94.67	gold quality
right frontal lobe	UBERON:0002810	94.67	gold quality
esophagus	UBERON:0001043	94.56	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.56	gold quality
left lobe of thyroid gland	UBERON:0001120	94.53	gold quality
stomach	UBERON:0000945	94.51	gold quality
apex of heart	UBERON:0002098	94.44	gold quality
vermiform appendix	UBERON:0001154	94.43	gold quality
fundus of stomach	UBERON:0001160	94.41	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.32
E-MTAB-9689	no	207.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting GLYR1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867

Literature-anchored findings (GeneRIF, showing 2)

• While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes. (PMID:30970244)
• Downregulation of GLYR1 contributes to microsatellite instability colorectal cancer by targeting p21 via the p38MAPK and PI3K/AKT pathways. (PMID:32370786)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	glyr1	ENSDARG00000099213
mus_musculus	Glyr1	ENSMUSG00000022536
rattus_norvegicus	Glyr1	ENSRNOG00000003065
drosophila_melanogaster	Ndf	FBGN0043456

Paralogs (1): HIBADH (ENSG00000106049)

Protein

Protein identifiers

Cytokine-like nuclear factor N-PAC — Q49A26 (reviewed: Q49A26)

Alternative names: 3-hydroxyisobutyrate dehydrogenase-like protein, Glyoxylate reductase 1 homolog, Nuclear protein NP60, Nuclear protein of 60 kDa, Nucleosome-destabilizing factor, Putative oxidoreductase GLYR1

All UniProt accessions (6): Q49A26, K7EK70, K7ELL0, K7EMM8, K7EPU6, K7EQB2

UniProt curated annotations — full annotation on UniProt →

Function. Cytokine-like nuclear factor with chromatin gene reader activity involved in chromatin modification and regulation of gene expression. Acts as a nucleosome-destabilizing factor that is recruited to genes during transcriptional activation. Recognizes and binds histone H3 without a preference for specific epigenetic markers and also binds DNA. Interacts with KDM1B and promotes its histone demethylase activity by facilitating the capture of H3 tails, they form a multifunctional enzyme complex that modifies transcribed chromatin and facilitates Pol II transcription through nucleosomes. Stimulates the acetylation of ‘Lys-56’ of nucleosomal histone H3 (H3K56ac) by EP300. With GATA4, co-binds a defined set of heart development genes and coregulates their expression during cardiomyocyte differentiation. Regulates p38 MAP kinase activity by mediating stress activation of MAPK14/p38alpha and specifically regulating MAPK14 signaling. Indirectly promotes phosphorylation of MAPK14 and activation of ATF2. The phosphorylation of MAPK14 requires upstream activity of MAP2K4 and MAP2K6.

Subunit / interactions. Homotetramere. Interacts with MAPK14. Interacts with KDM1B at nucleosomes; this interaction stimulates H3K4me1 and H3K4me2 demethylation. Binds to mononucleosomes. Interacts with GATA4; the interaction is required for a synergistic activation of GATA4 target genes transcription.

Subcellular location. Nucleus. Chromosome.

Domain organisation. The A.T hook DNA-binding domain is required for the interaction with MAPK14. The PWWP domain is a H3 reader and strongly binds DNA. In the dehydrogenase domain, the conserved NAD(P)H-binding sites and sequence similarity to plant dehydrogenases suggest that this protein may have oxidoreductase activity. However, since the active site is not conserved, the dehydrogenase domain seems to serve as a catalytically inert oligomerization module.

Similarity. Belongs to the HIBADH-related family. NP60 subfamily.

Isoforms (5)

UniProt ID	Names	Canonical?
Q49A26-1	1	yes
Q49A26-2	2
Q49A26-5	5
Q49A26-3	3
Q49A26-4	4

RefSeq proteins (5): NP_001295025, NP_001311025, NP_001311026, NP_001311027, NP_115958* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000313	PWWP_dom	Domain
IPR006115	6PGDH_NADP-bd	Domain
IPR008927	6-PGluconate_DH-like_C_sf	Homologous_superfamily
IPR013328	6PGD_dom2	Homologous_superfamily
IPR029154	HIBADH-like_NADP-bd	Domain
IPR035501	GLYR1_PWWP	Domain
IPR036291	NAD(P)-bd_dom_sf	Homologous_superfamily
IPR051265	HIBADH-related_NP60_sf	Family

Pfam: PF00855, PF03446, PF14833

UniProt features (72 total): helix 17, cross-link 10, strand 9, mutagenesis site 8, splice variant 4, region of interest 4, sequence variant 4, binding site 3, modified residue 3, sequence conflict 3, compositionally biased region 2, chain 1, domain 1, site 1, DNA-binding region 1, turn 1

Structure

Experimental structures (PDB)

8 structures.

PDB	Method	Resolution (Å)
4HSU	X-RAY DIFFRACTION	1.99
4GUT	X-RAY DIFFRACTION	2
4GUS	X-RAY DIFFRACTION	2.23
4GUU	X-RAY DIFFRACTION	2.3
2UYY	X-RAY DIFFRACTION	2.5
4GUR	X-RAY DIFFRACTION	2.51
6R1U	ELECTRON MICROSCOPY	4.36
6R25	ELECTRON MICROSCOPY	4.61

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q49A26-F1	77.79	0.59

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 217 (required to promote kdm1b demethylase activity toward histone h3k4me1 and h3k4me2)

Ligand- & substrate-binding residues (3): 362; 505; 271–285

Post-translational modifications (13): 130, 167, 540, 135, 176, 179, 201, 211, 227, 237, 240, 269, 302

Mutagenesis-validated functional residues (8):

Position	Phenotype
214	slightly reduced stimulation of kdm1b demethylase activity, but normal kdm1b-binding.
216	slightly reduced stimulation of kdm1b demethylase activity, but normal kdm1b-binding.
217	abolished stimulation of kdm1b demethylase activity, reduced affinity for histone h3 of the dimer with kdm1b, but normal
219	impaired kdm1b-binding and abolished stimulation of kdm1b demethylase activity; when associated with a-223.
220–222	impaired kdm1b-binding and abolished stimulation of kdm1b demethylase activity.
223	impaired kdm1b-binding and abolished stimulation of kdm1b demethylase activity; when associated with a-219.
437	loss of tetramerization and protein stability.
437	no effect on tetramerization or protein stability.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 149 (showing top): ELVIDGE_HYPOXIA_DN, CGGAARNGGCNG_UNKNOWN, CREBP1_Q2, CREB_Q4, TGTGTGA_MIR377, GRE_C, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_TRANSCRIPTION_INITIATION_AT_RNA_POLYMERASE_II_PROMOTER, ATF3_Q6, CREB_Q2_01, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, PU1_Q6, KIM_GASTRIC_CANCER_CHEMOSENSITIVITY, SENESE_HDAC1_TARGETS_UP, GOBP_CHROMATIN_REMODELING

GO Biological Process (2): transcription initiation-coupled chromatin remodeling (GO:0045815), transcription elongation-coupled chromatin remodeling (GO:0140673)

GO Molecular Function (9): DNA binding (GO:0003677), chromatin binding (GO:0003682), nucleosome binding (GO:0031491), histone binding (GO:0042393), NADP binding (GO:0050661), NAD binding (GO:0051287), chromatin-protein adaptor activity (GO:0140463), protein binding (GO:0005515), oxidoreductase activity (GO:0016491)

GO Cellular Component (6): chromatin (GO:0000785), nucleosome (GO:0000786), nucleoplasm (GO:0005654), cytosol (GO:0005829), nucleus (GO:0005634), chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
binding	2
chromatin binding	2
adenyl nucleotide binding	2
transcription initiation at RNA polymerase II promoter	1
positive regulation of gene expression, epigenetic	1
chromatin remodeling	1
transcription elongation by RNA polymerase II	1
nucleic acid binding	1
protein-containing complex binding	1
protein binding	1
chromatin organization	1
protein-macromolecule adaptor activity	1
catalytic activity	1
chromosome	1
chromatin	1
protein-DNA complex	1
nuclear lumen	1
cytoplasm	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

2758 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLYR1	MAP2K6	P52564	643
GLYR1	MAP2K4	P45985	493
GLYR1	NSD2	O96028	475
GLYR1	NSD1	Q96L73	474
GLYR1	MED16	Q9Y2X0	464
GLYR1	PACC1	Q9H813	443
GLYR1	ACTR3	P32391	442
GLYR1	BCLAF1	Q9NYF8	434
GLYR1	TBL2	Q9Y4P3	433
GLYR1	MSH6	P52701	424
GLYR1	CCT2	P78371	424
GLYR1	MAPK8	P45983	423
GLYR1	POLR2E	P19388	422
GLYR1	MAPK14	Q16539	414
GLYR1	UPF1	Q92900	403
GLYR1	SETD2	Q9BYW2	403

IntAct

237 interactions, top by confidence:

A	B	Type	Score
STK3	RASSF2	psi-mi:“MI:0914”(association)	0.950
MED4	MED19	psi-mi:“MI:0914”(association)	0.900
FHL2	GLYR1	psi-mi:“MI:0915”(physical association)	0.670
EIF1AD	GLYR1	psi-mi:“MI:0915”(physical association)	0.670
GLYR1	EIF1AD	psi-mi:“MI:0915”(physical association)	0.670
GLYR1	FHL2	psi-mi:“MI:0915”(physical association)	0.670
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
NOP53	RRP8	psi-mi:“MI:0914”(association)	0.640
NPM1	NVL	psi-mi:“MI:0914”(association)	0.610
CCNC	GLYR1	psi-mi:“MI:0915”(physical association)	0.560
GLYR1	CFAP206	psi-mi:“MI:0915”(physical association)	0.560
GLYR1	CCNC	psi-mi:“MI:0915”(physical association)	0.560
CFAP206	GLYR1	psi-mi:“MI:0915”(physical association)	0.560
RPL28	MAGEB2	psi-mi:“MI:0914”(association)	0.560
N	RBM47	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
ZC3HAV1	KHNYN	psi-mi:“MI:0914”(association)	0.530
MACROH2A2	PPM1G	psi-mi:“MI:0914”(association)	0.530
PPAN	PPM1G	psi-mi:“MI:0914”(association)	0.530
PRR11	NVL	psi-mi:“MI:0914”(association)	0.530
MAGEA1	MAGEB3	psi-mi:“MI:0914”(association)	0.530
H1-4	RRP8	psi-mi:“MI:0914”(association)	0.530
RPL30	RRP8	psi-mi:“MI:0914”(association)	0.530

BioGRID (307): GLYR1 (Two-hybrid), GLYR1 (Two-hybrid), GLYR1 (Two-hybrid), C6orf165 (Two-hybrid), GLYR1 (Protein-peptide), GLYR1 (Affinity Capture-MS), GLYR1 (Affinity Capture-MS), GLYR1 (Affinity Capture-MS), GLYR1 (Affinity Capture-MS), GLYR1 (Affinity Capture-MS), GLYR1 (Affinity Capture-MS), GLYR1 (Affinity Capture-MS), GLYR1 (Affinity Capture-MS), NEFH (Affinity Capture-MS), BLK (Affinity Capture-MS)

ESM2 similar proteins: A4FUF0, A4Q9F4, D2XV59, E1C1R4, O94888, O95267, P42694, P54198, P79987, Q15139, Q49A26, Q4R8V9, Q4SS66, Q562D5, Q5R372, Q5R5M3, Q5R7T2, Q5RDU9, Q5REY7, Q5RKH0, Q5RKN4, Q5T6S3, Q5ZIA0, Q5ZJ17, Q5ZLS2, Q5ZLS7, Q61666, Q62101, Q6DC64, Q6DFV5, Q6P5G6, Q6ZPY2, Q6ZWH5, Q70Z35, Q75Q39, Q80VL1, Q86W50, Q8BY87, Q8BYN5, Q8CIW5

Diamond homologs: A4FUF0, F4I907, F4K4D6, O75475, P51858, P51859, Q175F8, Q29NG1, Q32N87, Q3UMU9, Q49A26, Q562D5, Q5R7T2, Q5RKH0, Q5RKN4, Q5XXA9, Q5ZLS7, Q66T72, Q6K431, Q6P2L6, Q6P4K1, Q7Q161, Q7Z4V5, Q812D1, Q8MJG1, Q8MT36, Q8T079, Q8VHK7, Q922P9, Q923W4, Q925G1, Q99JF8, Q9BZ95, Q9FNE4, Q9JMG7, Q9LEY4, Q9LSV0, Q9LYZ0, Q9SF36, Q9SZE1

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
SPOP	“down-regulates quantity by destabilization”	GLYR1	binding
LUBAC	“down-regulates quantity by destabilization”	GLYR1	ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 188 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Formation of Senescence-Associated Heterochromatin Foci (SAHF)	7	44.0×	3e-09
Peptide chain elongation	22	26.1×	1e-23
Viral mRNA Translation	22	26.1×	1e-23
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	22	25.8×	1e-23
Transport of Mature Transcript to Cytoplasm	7	24.9×	2e-07
Selenocysteine synthesis	22	24.7×	2e-23
Eukaryotic Translation Termination	22	24.7×	2e-23
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	22	24.2×	3e-23

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of DNA recombination	6	41.6×	6e-07
chromosome condensation	6	31.2×	4e-06
regulation of mRNA splicing, via spliceosome	5	27.4×	7e-05
cytoplasmic translation	23	26.3×	9e-24
negative regulation of mRNA splicing, via spliceosome	5	23.6×	1e-04
ribosomal large subunit biogenesis	7	19.2×	8e-06
ribosomal small subunit biogenesis	12	16.9×	1e-09
rRNA processing	18	15.7×	2e-14

Disease & clinical

Clinical variants and AI predictions

ClinVar

87 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2665 predictions. Top by Δscore:

Variant	Effect	Δscore
16:4805308:CAC:C	acceptor_gain	1.0000
16:4805311:CTG:C	acceptor_loss	1.0000
16:4805312:T:C	acceptor_loss	1.0000
16:4811165:CCTA:C	donor_loss	1.0000
16:4811166:CTAC:C	donor_loss	1.0000
16:4811167:TAC:T	donor_loss	1.0000
16:4811168:A:AC	donor_gain	1.0000
16:4811168:ACCTC:A	donor_loss	1.0000
16:4811169:C:CC	donor_gain	1.0000
16:4811169:C:CG	donor_loss	1.0000
16:4811169:CCT:C	donor_gain	1.0000
16:4811290:GATAT:G	acceptor_gain	1.0000
16:4811291:ATAT:A	acceptor_gain	1.0000
16:4811292:TAT:T	acceptor_gain	1.0000
16:4811293:AT:A	acceptor_gain	1.0000
16:4811293:ATC:A	acceptor_loss	1.0000
16:4811294:TC:T	acceptor_loss	1.0000
16:4811295:C:CA	acceptor_loss	1.0000
16:4811295:C:CC	acceptor_gain	1.0000
16:4811296:T:C	acceptor_loss	1.0000
16:4811618:CTCA:C	donor_gain	1.0000
16:4811621:A:AC	donor_gain	1.0000
16:4811622:C:CG	donor_gain	1.0000
16:4811622:CT:C	donor_gain	1.0000
16:4811622:CTT:C	donor_gain	1.0000
16:4811622:CTTT:C	donor_gain	1.0000
16:4811623:TTTGG:T	donor_gain	1.0000
16:4811624:TTGGC:T	donor_gain	1.0000
16:4811800:CAC:C	acceptor_gain	1.0000
16:4811803:CTG:C	acceptor_loss	1.0000

AlphaMissense

3642 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:4805298:C:G	A534P	1.000
16:4811216:C:T	G514D	1.000
16:4811217:C:G	G514R	1.000
16:4811237:A:G	L507P	1.000
16:4811715:A:G	L457P	1.000
16:4811724:C:T	G454E	1.000
16:4811725:C:A	G454W	1.000
16:4811725:C:G	G454R	1.000
16:4811725:C:T	G454R	1.000
16:4811730:G:T	A452D	1.000
16:4811731:C:G	A452P	1.000
16:4811752:C:A	G445W	1.000
16:4811752:C:G	G445R	1.000
16:4811752:C:T	G445R	1.000
16:4812154:C:T	G405E	1.000
16:4817618:A:G	W296R	1.000
16:4817618:A:T	W296R	1.000
16:4817620:A:T	V295D	1.000
16:4817692:C:T	G271E	1.000
16:4832908:A:G	W54R	1.000
16:4832908:A:T	W54R	1.000
16:4846178:C:T	G24E	1.000
16:4846181:G:T	P23Q	1.000
16:4805258:A:T	V547E	0.999
16:4805262:C:G	A546P	0.999
16:4805270:T:A	D543V	0.999
16:4805271:C:G	D543H	0.999
16:4805297:G:T	A534D	0.999
16:4805302:T:A	K532N	0.999
16:4805302:T:G	K532N	0.999

dbSNP variants (sampled 300 via entrez): RS1000081041 (16:4823529 A>G), RS1000164195 (16:4843504 A>C), RS1000174386 (16:4816032 G>A,T), RS1000178227 (16:4812745 C>T), RS1000190972 (16:4804740 C>T), RS1000214530 (16:4843678 C>T), RS1000252593 (16:4843397 C>T), RS1000274835 (16:4811841 G>A), RS1000304261 (16:4812023 A>T), RS1000337924 (16:4815067 G>C), RS1000366021 (16:4831506 C>A,T), RS1000377974 (16:4835762 C>T), RS1000418334 (16:4806642 C>G), RS1000430138 (16:4823310 T>C), RS1000501279 (16:4842657 A>G)

Disease associations

OMIM: gene MIM:610660 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003542_157	Night sleep phenotypes	1.000000e-06
GCST005275_25	Cancer	3.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, increases methylation	3
sodium arsenite	increases abundance, increases expression	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
TAK-243	decreases sumoylation	1
2,4,6-tribromophenol	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
deoxynivalenol	decreases expression	1
testosterone undecanoate	affects cotreatment, increases expression	1
decabromobiphenyl ether	decreases expression	1
trichostatin A	increases expression	1
beta-lapachone	decreases expression	1
coumarin	decreases phosphorylation	1
ICG 001	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	increases expression	1
Vorinostat	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Caffeine	decreases phosphorylation	1
Diazinon	increases methylation	1
Dinitrochlorobenzene	affects binding	1
Ivermectin	decreases expression	1
Potassium Dichromate	increases expression	1
Smoke	decreases expression	1
Levonorgestrel	affects cotreatment, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2XS	Abcam HEK293T GLYR1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.