KRI1

Summary

KRI1 (KRI1 homolog, HGNC:25769) is a protein-coding gene on chromosome 19p13.2, encoding Protein KRI1 homolog (Q8N9T8). It is a common-essential gene (DepMap: required in 97.8% of cancer cell lines).

This gene overlaps with the gene for cysteine endopeptidase AUT-like 4 in a head-to-tail orientation.

Source: NCBI Gene 65095 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 157 total
• Cancer dependency (DepMap): dependent in 97.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_023008

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25769
Approved symbol	KRI1
Name	KRI1 homolog
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12949
Ensembl gene	ENSG00000129347
Ensembl biotype	protein_coding
OMIM	621355
Entrez	65095

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 9 protein_coding, 8 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000312962, ENST00000432197, ENST00000478863, ENST00000536689, ENST00000536714, ENST00000537363, ENST00000537433, ENST00000537964, ENST00000539027, ENST00000543682, ENST00000543842, ENST00000544397, ENST00000546063, ENST00000612875, ENST00000618579, ENST00000652042, ENST00000906782, ENST00000923422, ENST00000958127, ENST00000958128

RefSeq mRNA: 1 — MANE Select: NM_023008 NM_023008

CCDS: CCDS12242

Canonical transcript exons

ENST00000312962 — 19 exons

Exon	Start	End
ENSE00003468257	10557972	10558060
ENSE00003479706	10561667	10561716
ENSE00003494303	10565717	10565790
ENSE00003494975	10561791	10561845
ENSE00003499751	10557769	10557895
ENSE00003513606	10555087	10555185
ENSE00003523593	10561169	10561265
ENSE00003530742	10562729	10562837
ENSE00003539449	10564929	10565034
ENSE00003547204	10555285	10555349
ENSE00003612561	10565906	10566010
ENSE00003614403	10558164	10558239
ENSE00003621041	10560312	10560448
ENSE00003644465	10559359	10559529
ENSE00003674666	10561003	10561080
ENSE00003686517	10559613	10559708
ENSE00003784136	10557552	10557682
ENSE00003786780	10559810	10559936
ENSE00003850206	10553085	10554281

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 95.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.6622 / max 302.8872, expressed in 1793 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179152	18.6622	1793

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	95.00	gold quality
granulocyte	CL:0000094	94.38	gold quality
tendon of biceps brachii	UBERON:0008188	90.90	gold quality
right testis	UBERON:0004534	90.51	gold quality
left testis	UBERON:0004533	90.24	gold quality
lower esophagus mucosa	UBERON:0035834	89.94	gold quality
spleen	UBERON:0002106	89.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.35	gold quality
lymph node	UBERON:0000029	89.29	gold quality
testis	UBERON:0000473	89.25	gold quality
tendon	UBERON:0000043	89.17	gold quality
skin of abdomen	UBERON:0001416	88.88	gold quality
ventricular zone	UBERON:0003053	88.61	gold quality
medial globus pallidus	UBERON:0002477	88.52	gold quality
blood	UBERON:0000178	88.44	gold quality
vagina	UBERON:0000996	88.39	gold quality
skin of leg	UBERON:0001511	88.17	gold quality
calcaneal tendon	UBERON:0003701	88.09	gold quality
gastrocnemius	UBERON:0001388	88.02	gold quality
right ovary	UBERON:0002118	87.93	gold quality
right lobe of thyroid gland	UBERON:0001119	87.88	gold quality
leukocyte	CL:0000738	87.85	gold quality
monocyte	CL:0000576	87.81	gold quality
apex of heart	UBERON:0002098	87.72	gold quality
mononuclear cell	CL:0000842	87.70	gold quality
thymus	UBERON:0002370	87.70	gold quality
stromal cell of endometrium	CL:0002255	87.66	gold quality
ectocervix	UBERON:0012249	87.62	gold quality
esophagus mucosa	UBERON:0002469	87.59	gold quality
ganglionic eminence	UBERON:0004023	87.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting KRI1, 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-4455	100.00	65.48	1587
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-4518	98.12	66.82	1030
HSA-MIR-3691-3P	97.90	65.97	791

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 97.8% of screened cell lines, common-essential.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	kri1	ENSDARG00000075380
mus_musculus	Kri1	ENSMUSG00000035047
rattus_norvegicus	Kri1	ENSRNOG00000057447
drosophila_melanogaster	CG5645	FBGN0036254
caenorhabditis_elegans		WBGENE00010044

Protein

Protein identifiers

Protein KRI1 homolog — Q8N9T8 (reviewed: Q8N9T8)

All UniProt accessions (6): Q8N9T8, A0A494C108, F8WFC1, H0YFD2, H0YG91, H0YH26

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the KRI1 family.

RefSeq proteins (1): NP_075384* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018034	Kri1	Family
IPR024626	Kri1-like_C	Domain

Pfam: PF05178, PF12936

UniProt features (46 total): modified residue 15, compositionally biased region 8, sequence variant 8, region of interest 7, sequence conflict 7, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9T8-F1	70.68	0.18

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 (15): 91, 93, 94, 95, 97, 136, 141, 163, 171, 280, 281, 309, 622, 628, 639

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 91 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MATURATION_OF_5_8S_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GOBP_MATURATION_OF_5_8S_RRNA, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOCC_90S_PRERIBOSOME, GOCC_PRERIBOSOME, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_NUCLEOLUS, GOCC_RIBONUCLEOPROTEIN_COMPLEX, chr19p13

GO Biological Process (1): endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (2): nucleolus (GO:0005730), 90S preribosome (GO:0030686)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	1
maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	1
endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	1
nucleic acid binding	1
binding	1
nuclear lumen	1
intracellular membraneless organelle	1
preribosome	1
t-UTP complex	1

Protein interactions and networks

STRING

1814 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRI1	KRR1	Q13601	784
KRI1	UTP23	Q9BRU9	648
KRI1	KRIT1	O00522	643
KRI1	DDX52	Q9Y2R4	606
KRI1	RRP7A	Q9Y3A4	595
KRI1	PDCD11	Q14690	576
KRI1	RCL1	Q9Y2P8	557
KRI1	ESF1	Q9H501	553
KRI1	NOP14	P78316	531
KRI1	FCF1	Q9Y324	496
KRI1	CCM2	Q9BSQ5	474
KRI1	NAT10	Q9H0A0	449
KRI1	TCERG1	O14776	447
KRI1	CNOT9	Q92600	438
KRI1	PPP4R3C	Q6ZMV5	436

IntAct

261 interactions, top by confidence:

A	B	Type	Score
H2AX	PPM1G	psi-mi:“MI:0914”(association)	0.730
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
RPS6	IPO7	psi-mi:“MI:0914”(association)	0.530
H1-6	ZNF724	psi-mi:“MI:0914”(association)	0.530
H1-4	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
PDGFB	DKC1	psi-mi:“MI:0914”(association)	0.530
ZCRB1	DKC1	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
CBX6	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
H2AC20	PPM1G	psi-mi:“MI:0914”(association)	0.530
H1-4	RRP8	psi-mi:“MI:0914”(association)	0.530
E4F1	ZBTB24	psi-mi:“MI:0914”(association)	0.530
RPSA	RPS17	psi-mi:“MI:0914”(association)	0.530
ZNF764	SH3PXD2B	psi-mi:“MI:0914”(association)	0.530
MRPL18	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPS2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
KRR1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
H2BC26	PPM1G	psi-mi:“MI:0914”(association)	0.530
CSNK2A1	KRI1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
KRI1	SAFB	psi-mi:“MI:0915”(physical association)	0.400
TTN	KRI1	psi-mi:“MI:0915”(physical association)	0.400
Naa50	WDR46	psi-mi:“MI:0914”(association)	0.350
NOP56	C12orf43	psi-mi:“MI:0914”(association)	0.350
HNRNPU		psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350

BioGRID (276): KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Co-fractionation), MPHOSPH10 (Co-fractionation), SUPT16H (Co-fractionation), KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), KRI1 (Proximity Label-MS)

ESM2 similar proteins: A1A5P2, A6QNR1, A8WY26, D3ZND0, O15213, O59678, P27672, P78316, Q0V8M0, Q15050, Q24K12, Q28IV8, Q2KIH4, Q2KII6, Q3T0Q8, Q3T0Z5, Q3UFY0, Q4KLC4, Q5M985, Q5RAS1, Q5RJT2, Q5TAP6, Q5TJE7, Q5ZKM1, Q640M1, Q6EJB6, Q6P0I6, Q6PFJ1, Q8BK35, Q8IY81, Q8N9T8, Q8NEJ9, Q8R3N1, Q8VDQ9, Q96BZ8, Q96EU6, Q9BRP8, Q9BRR8, Q9BVJ6, Q9C086

Diamond homologs: P42846, Q0V8M0, Q6DRJ4, Q8N9T8, Q8VDQ9, Q9VTU0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 214 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
Eukaryotic Translation Initiation	13	29.5×	4e-15
Cap-dependent Translation Initiation	13	29.5×	4e-15
SARS-CoV-1 modulates host translation machinery	13	29.5×	4e-15
Eukaryotic Translation Elongation	13	26.6×	2e-14
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	13	26.0×	3e-14
Nonsense-Mediated Decay (NMD)	14	24.0×	8e-15
Peptide chain elongation	24	22.4×	3e-24
Viral mRNA Translation	24	22.4×	3e-24

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of DNA recombination	6	36.0×	2e-06
regulation of mRNA splicing, via spliceosome	6	28.5×	7e-06
chromosome condensation	6	27.0×	8e-06
cytoplasmic translation	25	24.8×	2e-25
ribosomal small subunit biogenesis	16	19.5×	3e-14
translation	25	13.7×	8e-19
rRNA processing	18	13.6×	2e-13
ribosomal large subunit biogenesis	5	11.9×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	126
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2612 predictions. Top by Δscore:

Variant	Effect	Δscore
19:10554277:CTGCC:C	acceptor_gain	1.0000
19:10554278:TGCC:T	acceptor_gain	1.0000
19:10554279:GCC:G	acceptor_gain	1.0000
19:10554280:CC:C	acceptor_gain	1.0000
19:10554280:CCC:C	acceptor_gain	1.0000
19:10554281:CC:C	acceptor_gain	1.0000
19:10554282:C:CC	acceptor_gain	1.0000
19:10554282:C:CG	acceptor_loss	1.0000
19:10554282:C:T	acceptor_gain	1.0000
19:10555082:CTTA:C	donor_loss	1.0000
19:10555083:TTA:T	donor_loss	1.0000
19:10555084:TA:T	donor_loss	1.0000
19:10555085:A:AC	donor_gain	1.0000
19:10555085:AC:A	donor_loss	1.0000
19:10555085:ACT:A	donor_gain	1.0000
19:10555086:C:CT	donor_gain	1.0000
19:10555086:CT:C	donor_gain	1.0000
19:10555086:CTC:C	donor_gain	1.0000
19:10555086:CTCT:C	donor_gain	1.0000
19:10555086:CTCTT:C	donor_gain	1.0000
19:10555181:CTGAC:C	acceptor_gain	1.0000
19:10555186:C:CC	acceptor_gain	1.0000
19:10555187:T:C	acceptor_loss	1.0000
19:10555348:ATCTG:A	acceptor_loss	1.0000
19:10555349:TC:T	acceptor_loss	1.0000
19:10555350:C:CC	acceptor_gain	1.0000
19:10555351:T:G	acceptor_loss	1.0000
19:10555354:G:C	acceptor_gain	1.0000
19:10557548:CTA:C	donor_loss	1.0000
19:10557550:ACCT:A	donor_gain	1.0000

AlphaMissense

4653 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:10557600:G:C	F523L	0.997
19:10557600:G:T	F523L	0.997
19:10557602:A:G	F523L	0.997
19:10559831:G:C	F302L	0.997
19:10559831:G:T	F302L	0.997
19:10559833:A:G	F302L	0.997
19:10555316:A:G	W551R	0.996
19:10555316:A:T	W551R	0.996
19:10559623:C:G	R338P	0.995
19:10555324:A:G	L548P	0.994
19:10557601:A:G	F523S	0.994
19:10565952:A:C	F16L	0.993
19:10565952:A:T	F16L	0.993
19:10565954:A:G	F16L	0.993
19:10557592:C:G	R526P	0.991
19:10559672:G:T	R322S	0.991
19:10559855:A:C	F294L	0.991
19:10559855:A:T	F294L	0.991
19:10559857:A:G	F294L	0.991
19:10557565:A:G	L535P	0.990
19:10559640:C:A	R332S	0.990
19:10559640:C:G	R332S	0.990
19:10565929:C:G	R24P	0.990
19:10555314:C:A	W551C	0.989
19:10555314:C:G	W551C	0.989
19:10559486:A:G	L356P	0.989
19:10559495:A:G	L353P	0.989
19:10559836:G:T	R301S	0.988
19:10559852:T:A	E295D	0.988
19:10559852:T:G	E295D	0.988

dbSNP variants (sampled 300 via entrez): RS1000006425 (19:10566701 CGGCCAA>C), RS1000285206 (19:10565066 C>T), RS1000369452 (19:10554133 G>A,T), RS1000557156 (19:10565692 TC>T), RS1001331701 (19:10564027 T>C), RS1001724982 (19:10565580 T>A,C,G), RS1001823372 (19:10564416 T>C), RS1002103261 (19:10565386 T>C), RS1002155710 (19:10565659 G>A,T), RS1002380985 (19:10556410 G>A), RS1002772244 (19:10562996 G>A), RS1002995597 (19:10566750 T>G), RS1003096792 (19:10561127 C>A,T), RS1003253400 (19:10567918 C>A), RS1003332777 (19:10566405 C>T)

Disease associations

OMIM: gene MIM:621355 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST90002379_193	Basophil count	1.000000e-19
GCST90002380_11	Basophil percentage of white cells	2.000000e-13
GCST90002389_390	Lymphocyte percentage of white cells	5.000000e-13
GCST90002390_521	Mean corpuscular hemoglobin	7.000000e-17
GCST90002392_60	Mean corpuscular volume	2.000000e-19
GCST90002394_440	Monocyte percentage of white cells	1.000000e-10
GCST90002398_82	Neutrophil count	2.000000e-18
GCST90002399_221	Neutrophil percentage of white cells	6.000000e-12
GCST90002403_277	Red blood cell count	5.000000e-09
GCST90002404_559	Red cell distribution width	5.000000e-15
GCST90002407_362	White blood cell count	5.000000e-11

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0005090	basophil count
EFO:0007992	basophil percentage of leukocytes
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0004527	mean corpuscular hemoglobin
EFO:0007989	monocyte percentage of leukocytes
EFO:0004833	neutrophil count
EFO:0007990	neutrophil percentage of leukocytes
EFO:0004305	erythrocyte count
EFO:0009188	Red cell distribution width

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	2
GSK-J4	decreases expression	1
FR900359	affects phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
Bortezomib	increases expression	1
Acrolein	increases abundance, affects cotreatment, decreases expression	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Diazinon	increases methylation	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ethyl Methanesulfonate	decreases expression	1
Hydrogen Peroxide	affects expression	1
Ivermectin	decreases expression	1
Ozone	affects cotreatment, decreases expression, increases abundance	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1
Vitamin K 3	affects expression	1
Volatile Organic Compounds	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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