H2BC13

Summary

H2BC13 (H2B clustered histone 13, HGNC:4748) is a protein-coding gene on chromosome 6p22.1, encoding Histone H2B type 1-L (Q99880). Core component of nucleosome. It is a selective cancer dependency (DepMap: 89.2% of cell lines).

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the small histone gene cluster on chromosome 6p22-p21.3.

Source: NCBI Gene 8340 — RefSeq curated summary.

At a glance

• GWAS associations: 21
• Clinical variants (ClinVar): 12 total
• Cancer dependency (DepMap): dependent in 89.2% of screened cell lines
• MANE Select transcript: NM_003519

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4748
Approved symbol	H2BC13
Name	H2B clustered histone 13
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Aliases	H2B/c, dJ97D16.4
Ensembl gene	ENSG00000185130
Ensembl biotype	protein_coding
OMIM	602800
Entrez	8340

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000377401

RefSeq mRNA: 1 — MANE Select: NM_003519 NM_003519

CCDS: CCDS4625

Canonical transcript exons

ENST00000377401 — 1 exons

Exon	Start	End
ENSE00001473797	27807479	27807929

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 97.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 235.8529 / max 8747.8987, expressed in 1746 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72380	235.8529	1746

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	97.09	gold quality
adrenal tissue	UBERON:0018303	84.34	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.18	gold quality
calcaneal tendon	UBERON:0003701	74.12	gold quality
colonic epithelium	UBERON:0000397	69.69	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	69.17	gold quality
bone marrow	UBERON:0002371	62.28	gold quality
tendon	UBERON:0000043	62.24	gold quality
lower esophagus mucosa	UBERON:0035834	61.93	gold quality
monocyte	CL:0000576	57.58	gold quality
tonsil	UBERON:0002372	57.00	gold quality
leukocyte	CL:0000738	56.84	gold quality
granulocyte	CL:0000094	53.61	gold quality
mucosa of transverse colon	UBERON:0004991	51.62	gold quality
ganglionic eminence	UBERON:0004023	51.49	gold quality
corpus callosum	UBERON:0002336	50.91	gold quality
blood	UBERON:0000178	50.53	gold quality
buccal mucosa cell	CL:0002336	50.23	gold quality
rectum	UBERON:0001052	49.53	gold quality
ventricular zone	UBERON:0003053	48.09	gold quality
middle temporal gyrus	UBERON:0002771	48.05	gold quality
lymph node	UBERON:0000029	43.51	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
hindlimb stylopod muscle	UBERON:0004252	42.90	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
descending thoracic aorta	UBERON:0002345	42.55	gold quality
transverse colon	UBERON:0001157	42.54	gold quality
uterine cervix	UBERON:0000002	42.53	gold quality
oviduct epithelium	UBERON:0004804	41.65	gold quality
urinary bladder	UBERON:0001255	41.59	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.75

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 89.2% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration. (PMID:22360420)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
mus_musculus	H2bc12	ENSMUSG00000062727
mus_musculus	H2bc7	ENSMUSG00000069268
mus_musculus	H2bc11	ENSMUSG00000069300
mus_musculus	H2bc24	ENSMUSG00000069303
mus_musculus	H2bc23	ENSMUSG00000069307
mus_musculus	H2bc13	ENSMUSG00000094338
mus_musculus	H2bc15	ENSMUSG00000095217

Paralogs (21): H2BW2 (ENSG00000101812), H2BW1 (ENSG00000123569), H2BC11 (ENSG00000124635), H2BC1 (ENSG00000146047), H2BC5 (ENSG00000158373), H2BC4 (ENSG00000180596), H2BC21 (ENSG00000184678), H2BC26 (ENSG00000196890), H2BC12 (ENSG00000197903), H2BC18 (ENSG00000203814), H2BC15 (ENSG00000233822), H2BC12L (ENSG00000234289), H2BC14 (ENSG00000273703), H2BC8 (ENSG00000273802), H2BC6 (ENSG00000274290), H2BC17 (ENSG00000274641), H2BC9 (ENSG00000275713), H2BC3 (ENSG00000276410), H2BC7 (ENSG00000277224), H2BC10 (ENSG00000278588), H2BK1 (ENSG00000285480)

Protein

Protein identifiers

Histone H2B type 1-L — Q99880 (reviewed: Q99880)

Alternative names: Histone H2B.c

All UniProt accessions (1): Q99880

UniProt curated annotations — full annotation on UniProt →

Function. Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Subunit / interactions. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.

Subcellular location. Nucleus. Chromosome.

Post-translational modifications. Monoubiquitination at Lys-35 (H2BK34Ub) by the MSL1/MSL2 dimer is required for histone H3 ‘Lys-4’ (H3K4me) and ‘Lys-79’ (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination at Lys-121 (H2BK120Ub) by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 ‘Lys-4’ and ‘Lys-79’ methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons. Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription. Phosphorylated on Ser-15 (H2BS14ph) by STK4/MST1 during apoptosis; which facilitates apoptotic chromatin condensation. Also phosphorylated on Ser-15 in response to DNA double strand breaks (DSBs), and in correlation with somatic hypermutation and immunoglobulin class-switch recombination. GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes. ADP-ribosylated by PARP1 or PARP2 on Ser-7 (H2BS6ADPr) in response to DNA damage. H2BS6ADPr promotes recruitment of CHD1L. Mono-ADP-ribosylated on Glu-3 (H2BE2ADPr) by PARP3 in response to single-strand breaks. Poly ADP-ribosylation on Glu-36 (H2BE35ADPr) by PARP1 regulates adipogenesis: it inhibits phosphorylation at Ser-37 (H2BS36ph), thereby blocking expression of pro-adipogenetic genes. Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes. Lactylated in macrophages by EP300/P300 by using lactoyl-CoA directly derived from endogenous or exogenous lactate, leading to stimulates gene transcription.

Similarity. Belongs to the histone H2B family.

RefSeq proteins (1): NP_003510* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000558	Histone_H2B	Family
IPR007125	H2A/H2B/H3	Domain
IPR009072	Histone-fold	Homologous_superfamily
IPR055333	HISTONE_H2B_site	Conserved_site

Pfam: PF00125

UniProt features (101 total): modified residue 91, cross-link 4, initiator methionine 1, chain 1, sequence variant 1, region of interest 1, compositionally biased region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99880-F1	87.45	0.69

Functional residue map

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

Post-translational modifications (95): 6, 6, 6, 6, 7, 12, 12, 12, 12, 12, 12, 13, 13, 13, 15, 16, 16, 16, 16, 17 …

Glycosylation sites (1): 113

Function

Pathways and Gene Ontology

Reactome pathways

58 pathways

ID	Pathway
R-HSA-110328	Recognition and association of DNA glycosylase with site containing an affected pyrimidine
R-HSA-110329	Cleavage of the damaged pyrimidine
R-HSA-110330	Recognition and association of DNA glycosylase with site containing an affected purine
R-HSA-110331	Cleavage of the damaged purine
R-HSA-1221632	Meiotic synapsis
R-HSA-171306	Packaging Of Telomere Ends
R-HSA-1912408	Pre-NOTCH Transcription and Translation
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex
R-HSA-212300	PRC2 methylates histones and DNA
R-HSA-2299718	Condensation of Prophase Chromosomes
R-HSA-2559580	Oxidative Stress Induced Senescence
R-HSA-2559582	Senescence-Associated Secretory Phenotype (SASP)
R-HSA-2559586	DNA Damage/Telomere Stress Induced Senescence
R-HSA-3214815	HDACs deacetylate histones
R-HSA-3214847	HATs acetylate histones
R-HSA-427359	SIRT1 negatively regulates rRNA expression
R-HSA-427389	ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427413	NoRC negatively regulates rRNA expression
R-HSA-5250924	B-WICH complex positively regulates rRNA expression
R-HSA-5334118	DNA methylation
R-HSA-5578749	Transcriptional regulation by small RNAs
R-HSA-5617472	Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-5625886	Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-5689880	Ub-specific processing proteases
R-HSA-5693565	Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-HSA-5693571	Nonhomologous End-Joining (NHEJ)
R-HSA-5693607	Processing of DNA double-strand break ends
R-HSA-606279	Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-68616	Assembly of the ORC complex at the origin of replication
R-HSA-69473	G2/M DNA damage checkpoint

MSigDB gene sets: 254 (showing top): REACTOME_MEIOTIC_RECOMBINATION, REACTOME_DNA_REPLICATION, REACTOME_SIGNALING_BY_NOTCH, GOBP_ANTIMICROBIAL_HUMORAL_RESPONSE, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_MEIOTIC_SYNAPSIS, XU_GH1_AUTOCRINE_TARGETS_UP, FISCHER_G1_S_CELL_CYCLE, REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_ORGAN_OR_TISSUE_SPECIFIC_IMMUNE_RESPONSE, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, MARTINEZ_RB1_TARGETS_DN

GO Biological Process (1): nucleosome assembly (GO:0006334)

GO Molecular Function (4): DNA binding (GO:0003677), structural constituent of chromatin (GO:0030527), protein heterodimerization activity (GO:0046982), protein binding (GO:0005515)

GO Cellular Component (6): nucleosome (GO:0000786), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), extracellular exosome (GO:0070062), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-12 pathways:

Category	Pathways
Cellular Senescence	3
Depyrimidination	2
Depurination	2
Epigenetic regulation of gene expression	2
Chromatin modifying enzymes	2
Negative epigenetic regulation of rRNA expression	2
Positive epigenetic regulation of rRNA expression	2
Meiosis	1
Telomere Maintenance	1
Pre-NOTCH Expression and Processing	1
TCF dependent signaling in response to WNT	1
Mitotic Prophase	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
chromatin	2
cellular anatomical structure	2
chromatin organization	1
nucleosome organization	1
protein-DNA complex assembly	1
nucleic acid binding	1
structural molecule activity	1
protein dimerization activity	1
binding	1
protein-DNA complex	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
extracellular vesicle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

2244 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
H2BC13	PLG	P00747	867
H2BC13	RNF20	Q5VTR2	842
H2BC13	H3C1	P02295	835
H2BC13	H3C14	Q71DI3	814
H2BC13	H3-5	Q6NXT2	812
H2BC13	H3-4	Q16695	812
H2BC13	H3-7	Q5TEC6	812
H2BC13	H3-3A	P06351	811
H2BC13	RNF40	O75150	772
H2BC13	H4C16	P02304	748
H2BC13	H4C7	Q99525	746
H2BC13	H2AC20	Q16777	736
H2BC13	H2AC19	P20670	735
H2BC13	USP22	Q9UPT9	727
H2BC13	DET1	Q7L5Y6	727

IntAct

84 interactions, top by confidence:

A	B	Type	Score
OSBPL9	VAPB	psi-mi:“MI:0914”(association)	0.790
RECQL	PARP1	psi-mi:“MI:0914”(association)	0.750
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
H2BC1	PPM1G	psi-mi:“MI:0914”(association)	0.640
MAPK7	PFDN6	psi-mi:“MI:0914”(association)	0.640
H2BC13	H2AB2	psi-mi:“MI:0915”(physical association)	0.560
AP2M1	H2BC13	psi-mi:“MI:0915”(physical association)	0.560
H2AB2	H2BC13	psi-mi:“MI:0915”(physical association)	0.560
GRB2	ARHGEF35	psi-mi:“MI:0914”(association)	0.530
NUFIP1	PDE2A	psi-mi:“MI:0914”(association)	0.530
H2BC26	PPM1G	psi-mi:“MI:0914”(association)	0.530
TONSL	H2AC4	psi-mi:“MI:0914”(association)	0.530
TMEM196	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
H2BC13	H4C16	psi-mi:“MI:0915”(physical association)	0.400
POLL	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
H2AC4	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
JPH2	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
NOP53	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
ZNF469	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
KIF21A	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
H3-4	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
NUP50	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
SMG5	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
ATAD5	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
H3C13	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
CEP78	H2BC13	psi-mi:“MI:0915”(physical association)	0.400
MAGIX	H2BC13	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (456): HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS)

ESM2 similar proteins: O60814, P02281, P02284, P04255, P06899, P06900, P07794, P0C1H3, P0C1H4, P0C1H5, P10853, P10854, P14001, P16889, P21897, P23527, P33778, P57053, P58876, P62807, P62808, P69069, P69070, Q16778, Q27484, Q27876, Q27894, Q2M2T1, Q2PFX4, Q32L48, Q5BJA5, Q5QNW6, Q5R893, Q5RCP8, Q64475, Q64478, Q64524, Q64525, Q6PC60, Q6ZWY9

Diamond homologs: A0A2R8Y619, A2WKT1, A2WKT4, A2WWU2, A2XF66, A2YWI3, A3AGM4, O22582, O60814, O65819, P02281, P02283, P02284, P02285, P02286, P02287, P02288, P02289, P02290, P04255, P06145, P06899, P06900, P07794, P07795, P0C1H3, P0C1H4, P0C1H5, P10853, P10854, P14001, P16888, P16889, P16890, P17271, P19374, P21897, P23527, P27326, P27807

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
SLBP	“up-regulates quantity by expression”	H2BC13	“translation regulation”
“MSL acetyltransferase”	“down-regulates activity”	H2BC13	monoubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 95 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
Packaging Of Telomere Ends	7	24.4×	1e-06
Recognition and association of DNA glycosylase with site containing an affected purine	7	22.7×	2e-06
Cleavage of the damaged purine	7	22.7×	2e-06
Replacement of protamines by nucleosomes in the male pronucleus	5	21.6×	4e-05
Recognition and association of DNA glycosylase with site containing an affected pyrimidine	7	20.5×	2e-06
Cleavage of the damaged pyrimidine	7	20.5×	2e-06
RNA Polymerase I Promoter Opening	7	20.5×	2e-06
ChAHP complex assembly	7	20.5×	2e-06

GO biological processes:

GO term	Partners	Fold	FDR
nucleosome assembly	6	10.3×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

109 predictions. Top by Δscore:

Variant	Effect	Δscore
6:27807800:T:A	donor_gain	0.8100
6:27807787:CA:C	donor_gain	0.7200
6:27807786:A:AC	donor_gain	0.6700
6:27807787:C:CC	donor_gain	0.6700
6:27807768:TCAGC:T	donor_gain	0.6400
6:27807826:G:A	donor_gain	0.5900
6:27807767:TTCAG:T	donor_gain	0.5800
6:27807728:ATGG:A	donor_gain	0.5700
6:27807830:T:TA	donor_gain	0.5700
6:27807734:T:C	acceptor_gain	0.5600
6:27807796:G:C	donor_gain	0.5600
6:27807747:CGG:C	acceptor_gain	0.5400
6:27807770:A:AC	donor_gain	0.5300
6:27807734:T:TC	acceptor_gain	0.5200
6:27807734:T:TG	acceptor_gain	0.5000
6:27807822:T:TA	donor_gain	0.5000
6:27807528:A:AC	donor_gain	0.4800
6:27807529:C:CC	donor_gain	0.4800
6:27807776:T:TG	acceptor_gain	0.4800
6:27807732:CCT:C	acceptor_gain	0.4600
6:27807546:TGGTG:T	donor_gain	0.4500
6:27807772:C:T	donor_gain	0.4500
6:27807733:CT:C	acceptor_gain	0.4100
6:27807760:G:T	donor_gain	0.4000
6:27807735:T:A	acceptor_gain	0.3800
6:27807782:ACGT:A	donor_loss	0.3800
6:27807783:CGTA:C	donor_loss	0.3800
6:27807784:G:GC	donor_loss	0.3800
6:27807786:A:AT	donor_loss	0.3800
6:27807787:C:A	donor_loss	0.3800

AlphaMissense

814 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:27807563:C:T	G115D	1.000
6:27807564:C:G	G115R	1.000
6:27807554:G:T	A118D	0.999
6:27807555:C:G	A118P	0.999
6:27807556:C:A	K117N	0.999
6:27807556:C:G	K117N	0.999
6:27807564:C:A	G115C	0.999
6:27807575:G:T	A111E	0.999
6:27807576:C:G	A111P	0.999
6:27807577:G:C	H110Q	0.999
6:27807577:G:T	H110Q	0.999
6:27807579:G:C	H110D	0.999
6:27807580:C:A	K109N	0.999
6:27807580:C:G	K109N	0.999
6:27807584:G:T	A108D	0.999
6:27807587:A:G	L107P	0.999
6:27807587:A:T	L107Q	0.999
6:27807593:C:A	G105V	0.999
6:27807593:C:T	G105E	0.999
6:27807594:C:A	G105W	0.999
6:27807605:A:G	L101P	0.999
6:27807609:G:T	R100S	0.999
6:27807614:G:T	A98D	0.999
6:27807615:C:G	A98P	0.999
6:27807619:C:A	Q96H	0.999
6:27807619:C:G	Q96H	0.999
6:27807627:C:T	E94K	0.999
6:27807628:C:A	R93S	0.999
6:27807628:C:G	R93S	0.999
6:27807629:C:A	R93M	0.999

dbSNP variants (sampled 300 via entrez): RS1003461925 (6:27808757 C>A,T), RS1005508169 (6:27808238 A>G), RS1005703886 (6:27807472 A>G), RS1006375060 (6:27809662 G>A), RS1006594923 (6:27808065 T>C), RS1007567119 (6:27808843 T>C), RS1009690976 (6:27808599 G>A), RS1011227710 (6:27807802 C>T), RS1012410462 (6:27807436 C>G), RS1012425848 (6:27809078 A>G), RS1013698568 (6:27809904 C>A,T), RS1013789275 (6:27809790 A>G), RS1016178436 (6:27809406 G>A), RS1016514772 (6:27809415 T>G), RS1016987591 (6:27809133 T>C)

Disease associations

OMIM: gene MIM:602800 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

21 associations (top):

Study	Trait	p-value
GCST003984_13	Parkinson’s disease	2.000000e-10
GCST004521_112	Autism spectrum disorder or schizophrenia	3.000000e-26
GCST004521_115	Autism spectrum disorder or schizophrenia	3.000000e-16
GCST004521_116	Autism spectrum disorder or schizophrenia	3.000000e-16
GCST004521_166	Autism spectrum disorder or schizophrenia	4.000000e-24
GCST004521_22	Autism spectrum disorder or schizophrenia	2.000000e-11
GCST004521_6	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_73	Autism spectrum disorder or schizophrenia	8.000000e-11
GCST004748_89	Lung cancer	2.000000e-10
GCST007507_10	Benign prostatic hyperplasia and lower urinary tract symptoms	4.000000e-17
GCST008921_6	Asthma and major depressive disorder	1.000000e-09
GCST010002_50	Refractive error	4.000000e-34
GCST010083_66	Hemoglobin levels	7.000000e-52
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0008008	lower urinary tract symptom
EFO:0004509	hemoglobin measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Benzo(a)pyrene	decreases expression, increases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
bisphenol A	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
polyhexamethyleneguanidine	affects expression	1
fenpyroximate	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1
dimethylarsinous acid	increases expression	1
pyrimidifen	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
jinfukang	increases expression	1
incobotulinumtoxinA	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases expression, increases abundance	1
Berberine	decreases expression	1
Cisplatin	decreases expression	1
Estradiol	affects expression	1
N-Nitrosopyrrolidine	decreases expression	1
Oxygen	decreases expression	1
Silicon Dioxide	increases expression	1
Urethane	decreases expression	1
Zinc	decreases expression	1
Lithium Chloride	decreases expression	1
Copper Sulfate	increases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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