QSER1

Summary

QSER1 (glutamine and serine rich 1, HGNC:26154) is a protein-coding gene on chromosome 11p13, encoding Glutamine and serine-rich protein 1 (Q2KHR3). Plays an essential role in the protection and maintenance of transcriptional and developmental programs.

Predicted to be located in chromosome.

Source: NCBI Gene 79832 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 240 total
• MANE Select transcript: NM_001076786

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26154
Approved symbol	QSER1
Name	glutamine and serine rich 1
Location	11p13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21924
Ensembl gene	ENSG00000060749
Ensembl biotype	protein_coding
OMIM	619440
Entrez	79832

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000524678, ENST00000527250, ENST00000527788, ENST00000528034, ENST00000528155, ENST00000650167

RefSeq mRNA: 5 — MANE Select: NM_001076786 NM_001076786, NM_001416036, NM_001416037, NM_001416038, NM_001416039

CCDS: CCDS41631

Canonical transcript exons

ENST00000650167 — 13 exons

Exon	Start	End
ENSE00000709696	32955296	32955412
ENSE00000709700	32955988	32956121
ENSE00000824356	32953857	32954179
ENSE00001316647	32957869	32958086
ENSE00001596529	32969046	32969143
ENSE00001752735	32931743	32935435
ENSE00001760464	32973397	32973549
ENSE00001783565	32975248	32975343
ENSE00002723727	32966300	32966437
ENSE00003832965	32927962	32928123
ENSE00003834907	32892811	32893334
ENSE00003835939	32927157	32927269
ENSE00003839098	32976334	32980270

Expression profiles

Bgee: expression breadth ubiquitous, 266 present calls, max score 98.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.0297 / max 262.9583, expressed in 1796 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113641	9.8752	1735
113639	7.6545	1699
113640	0.8810	519
113644	0.4290	212
113642	0.1901	64

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
caput epididymis	UBERON:0004358	98.04	gold quality
corpus epididymis	UBERON:0004359	97.47	gold quality
tibia	UBERON:0000979	97.38	gold quality
cauda epididymis	UBERON:0004360	96.83	gold quality
germinal epithelium of ovary	UBERON:0001304	96.80	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.67	gold quality
superior surface of tongue	UBERON:0007371	96.39	gold quality
parietal pleura	UBERON:0002400	96.13	gold quality
esophagus squamous epithelium	UBERON:0006920	95.90	gold quality
skin of hip	UBERON:0001554	95.83	gold quality
visceral pleura	UBERON:0002401	95.68	gold quality
pigmented layer of retina	UBERON:0001782	95.57	gold quality
oral cavity	UBERON:0000167	95.24	gold quality
gingiva	UBERON:0001828	94.91	gold quality
ganglionic eminence	UBERON:0004023	94.87	gold quality
trigeminal ganglion	UBERON:0001675	94.69	gold quality
pharyngeal mucosa	UBERON:0000355	94.67	gold quality
superficial temporal artery	UBERON:0001614	94.64	gold quality
gingival epithelium	UBERON:0001949	94.55	gold quality
pleura	UBERON:0000977	94.40	gold quality
biceps brachii	UBERON:0001507	94.23	gold quality
upper leg skin	UBERON:0004262	94.00	gold quality
body of tongue	UBERON:0011876	93.71	gold quality
mammary duct	UBERON:0001765	93.50	gold quality
saphenous vein	UBERON:0007318	93.23	gold quality
mammalian vulva	UBERON:0000997	92.90	gold quality
palpebral conjunctiva	UBERON:0001812	92.63	gold quality
superior vestibular nucleus	UBERON:0007227	92.43	gold quality
pericardium	UBERON:0002407	92.40	gold quality
tongue	UBERON:0001723	91.92	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.51

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• QSER1 protects DNA methylation valleys from de novo methylation. (PMID:33833093)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	qser1	ENSDARG00000074750
mus_musculus	Qser1	ENSMUSG00000074994
rattus_norvegicus	Qser1	ENSRNOG00000037514

Paralogs (1): PRR12 (ENSG00000126464)

Protein

Protein identifiers

Glutamine and serine-rich protein 1 — Q2KHR3 (reviewed: Q2KHR3)

All UniProt accessions (3): A0A3B3IRW6, A0A3B3ISY4, H0YCQ7

UniProt curated annotations — full annotation on UniProt →

Function. Plays an essential role in the protection and maintenance of transcriptional and developmental programs. Protects many bivalent promoters and poised enhancers from hypermethylation, showing a marked preference for these regulatory elements over other types of promoters or enhancers. Mechanistically, cooperates with TET1 and binds to DNA in a common complex to inhibit the binding of DNMT3A/3B and therefore de novo methylation.

Subunit / interactions. Interacts with TET1.

Subcellular location. Chromosome.

Isoforms (2)

UniProt ID	Names	Canonical?
Q2KHR3-1	1	yes
Q2KHR3-2	2

RefSeq proteins (5): NP_001070254, NP_001402965, NP_001402966, NP_001402967, NP_001402968 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025451	DUF4211	Domain
IPR052466	DNA_MethProtect_Complex	Family

Pfam: PF13926

UniProt features (43 total): modified residue 12, region of interest 9, compositionally biased region 8, sequence conflict 5, sequence variant 4, cross-link 2, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2KHR3-F1	44.34	0.11

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 (14): 1, 586, 615, 886, 949, 987, 1211, 1230, 1231, 1239, 1341, 1348, 1058, 1083

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 207 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, MODULE_255, GCM_ZNF198, MODULE_317, WEI_MYCN_TARGETS_WITH_E_BOX, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, TTGGAGA_MIR5155P_MIR519E, SANSOM_APC_TARGETS_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, RYTTCCTG_ETS2_B, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, HAN_SATB1_TARGETS_DN, CTTTGTA_MIR524, MODULE_69

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	1

Protein interactions and networks

STRING

798 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
QSER1	TCP11L1	Q9NUJ3	618
QSER1	CCDC73	Q6ZRK6	612
QSER1	CSTF3	Q12996	581
QSER1	PRRG4	Q9BZD6	561
QSER1	FAXC	Q5TGI0	556
QSER1	DEPDC7	Q96QD5	541
QSER1	PROSER1	Q86XN7	477
QSER1	RET	P07949	475
QSER1	AMPD2	Q01433	465
QSER1	DSTYK	Q6XUX3	460
QSER1	NUFIP2	Q7Z417	456
QSER1	EIF3M	Q7L2H7	455
QSER1	DEFB134	Q4QY38	454
QSER1	IWS1	Q96ST2	450
QSER1	TMTC2	Q8N394	446

IntAct

85 interactions, top by confidence:

A	B	Type	Score
FOXP1	FOXP2	psi-mi:“MI:0914”(association)	0.910
COMMD8	VPS26C	psi-mi:“MI:0914”(association)	0.640
BCOR	CBX4	psi-mi:“MI:0914”(association)	0.530
PCGF1	CBX4	psi-mi:“MI:0914”(association)	0.530
MAGEA10	POTEF	psi-mi:“MI:0914”(association)	0.530
FHL2	CNOT1	psi-mi:“MI:0914”(association)	0.530
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
EN1	NFIB	psi-mi:“MI:2364”(proximity)	0.470
QSER1	F2RL1	psi-mi:“MI:0915”(physical association)	0.370
Fam83d	SEC16A	psi-mi:“MI:0914”(association)	0.350
MAGEA10	XPO1	psi-mi:“MI:0914”(association)	0.350
FOXJ2	TCERG1	psi-mi:“MI:0914”(association)	0.350
BRD1	MRPS14	psi-mi:“MI:0914”(association)	0.350
PB2	HAX1	psi-mi:“MI:0914”(association)	0.350
PB2	SEC16A	psi-mi:“MI:0914”(association)	0.350
PB2	PIK3R2	psi-mi:“MI:0914”(association)	0.350
PB1	ESYT2	psi-mi:“MI:0914”(association)	0.350
PB1		psi-mi:“MI:0914”(association)	0.350
PB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
PB2	IPO5	psi-mi:“MI:0914”(association)	0.350
MKI67	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
SOX2	DDX39A	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
BRD2	DNAJA2	psi-mi:“MI:0914”(association)	0.350
DNAJB6	HSPA8	psi-mi:“MI:0914”(association)	0.350
H2BC21	SMCHD1	psi-mi:“MI:0914”(association)	0.350
PSPC1	MCRIP1	psi-mi:“MI:0914”(association)	0.350
hspa1a_hspa1b_human-1	SHTN1	psi-mi:“MI:0914”(association)	0.350
CALML3	MYO1C	psi-mi:“MI:0914”(association)	0.350

BioGRID (135): QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), QSER1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTH6, A0A1D5RMD1, A1KXM5, A2AEY4, A6NCI8, A6QQS3, A7KBS4, C4P6S0, O94713, P0C9Z7, P53963, P53976, Q0P670, Q0VAV2, Q10668, Q196W1, Q2KHR3, Q2YDJ5, Q32MG2, Q3V0A6, Q3V3Q4, Q4V8E9, Q5JRM2, Q68FV4, Q6AXV6, Q6AYN3, Q6NS59, Q7TSG5, Q80VJ6, Q80Y39, Q80YD3, Q810T2, Q86XD8, Q8C5U4, Q8CH19, Q8IWI9, Q8K4E0, Q8NDH2, Q8NEV8, Q8NFU7

Diamond homologs: A0A338P6K9, E9PYL2, Q2KHR3, Q66IN2, Q9ULL5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 117 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.

GO biological processes:

GO term	Partners	Fold	FDR
chromatin remodeling	11	7.4×	8e-05
gene expression	8	5.9×	7e-03
transcription by RNA polymerase II	9	5.9×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	208
Likely benign	16
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2456 predictions. Top by Δscore:

Variant	Effect	Δscore
11:32893332:CAGGT:C	donor_loss	1.0000
11:32893333:AGGT:A	donor_loss	1.0000
11:32893334:GGTA:G	donor_loss	1.0000
11:32893336:T:A	donor_loss	1.0000
11:32927155:A:AG	acceptor_gain	1.0000
11:32927156:G:GG	acceptor_gain	1.0000
11:32928079:G:GT	donor_gain	1.0000
11:32953853:TCAG:T	acceptor_loss	1.0000
11:32953854:CAGAA:C	acceptor_gain	1.0000
11:32953855:A:AG	acceptor_gain	1.0000
11:32953856:G:A	acceptor_loss	1.0000
11:32953856:G:GA	acceptor_gain	1.0000
11:32953856:GA:G	acceptor_gain	1.0000
11:32953856:GAA:G	acceptor_gain	1.0000
11:32953938:T:G	donor_gain	1.0000
11:32953973:G:GG	donor_gain	1.0000
11:32954121:GCCAA:G	donor_gain	1.0000
11:32955294:A:AG	acceptor_gain	1.0000
11:32955294:AGGAG:A	acceptor_gain	1.0000
11:32955295:G:GG	acceptor_gain	1.0000
11:32955295:GGA:G	acceptor_gain	1.0000
11:32955295:GGAGG:G	acceptor_gain	1.0000
11:32955408:ATAGT:A	donor_gain	1.0000
11:32955409:TAGT:T	donor_gain	1.0000
11:32955411:GT:G	donor_gain	1.0000
11:32955412:TGTA:T	donor_loss	1.0000
11:32955413:G:GG	donor_gain	1.0000
11:32955413:GTAA:G	donor_loss	1.0000
11:32955414:T:A	donor_loss	1.0000
11:32955982:CCTCA:C	acceptor_loss	1.0000

AlphaMissense

12150 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:32955332:T:A	W1384R	0.999
11:32955332:T:C	W1384R	0.999
11:32955345:A:T	K1388I	0.999
11:32955351:T:C	L1390S	0.999
11:32956073:T:A	V1439D	0.999
11:32966384:T:C	L1556P	0.999
11:32966387:T:A	V1557D	0.999
11:32973499:T:G	Y1641D	0.999
11:32975300:T:C	L1675P	0.999
11:32975332:T:C	C1686R	0.999
11:32975334:T:G	C1686W	0.999
11:32976383:T:A	V1706D	0.999
11:32976443:T:C	L1726P	0.999
11:32935103:T:C	F1153S	0.998
11:32935115:T:C	L1157P	0.998
11:32955354:T:C	L1391S	0.998
11:32955995:G:A	G1413E	0.998
11:32966389:A:C	S1558R	0.998
11:32966391:C:A	S1558R	0.998
11:32966391:C:G	S1558R	0.998
11:32966395:G:C	A1560P	0.998
11:32966396:C:A	A1560D	0.998
11:32975290:T:G	Y1672D	0.998
11:32975300:T:A	L1675H	0.998
11:32975305:C:G	H1677D	0.998
11:32975306:A:C	H1677P	0.998
11:32975307:T:A	H1677Q	0.998
11:32975307:T:G	H1677Q	0.998
11:32975314:T:G	Y1680D	0.998
11:32975333:G:A	C1686Y	0.998

dbSNP variants (sampled 300 via entrez): RS1000016202 (11:32946152 A>T), RS1000034043 (11:32901133 G>A), RS1000083457 (11:32896002 G>A,C), RS1000115603 (11:32972394 A>G), RS1000172765 (11:32927469 G>A), RS1000180321 (11:32949731 C>A,T), RS1000216635 (11:32894097 T>C), RS1000247717 (11:32893880 G>C), RS1000253109 (11:32914422 G>C,T), RS1000301719 (11:32920858 A>G), RS1000337388 (11:32907390 A>G), RS1000531604 (11:32947892 T>G), RS1000541720 (11:32929868 T>C), RS1000546417 (11:32902156 C>T), RS1000602847 (11:32895293 G>A)

Disease associations

OMIM: gene MIM:619440 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000490_4	Parkinson’s disease (age of onset)	5.000000e-07
GCST009379_310	Type 2 diabetes	9.000000e-06
GCST009379_311	Type 2 diabetes	2.000000e-10
GCST009379_312	Type 2 diabetes	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004847	age at onset

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
Valproic Acid	affects expression, decreases expression	5
trichostatin A	affects expression, decreases expression	2
Estradiol	increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
glycidyl methacrylate	increases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
coumarin	increases phosphorylation	1
abrine	decreases expression	1
jinfukang	decreases expression	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Caffeine	decreases phosphorylation	1
Coumestrol	affects cotreatment, increases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Formaldehyde	decreases expression	1
Nickel	decreases expression	1
Plant Oils	increases expression	1
Dihydrotestosterone	increases expression	1
Dronabinol	increases expression	1

Clinical trials (associated diseases)

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