KRCC1

Summary

KRCC1 (lysine rich coiled-coil 1, HGNC:28039) is a protein-coding gene on chromosome 2p11.2, encoding Lysine-rich coiled-coil protein 1 (Q9NPI7). Regulates CHEK1-mediated cell cycle checkpoint.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 41 total — 1 pathogenic
• MANE Select transcript: NM_016618

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28039
Approved symbol	KRCC1
Name	lysine rich coiled-coil 1
Location	2p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22333
Ensembl gene	ENSG00000172086
Ensembl biotype	protein_coding
OMIM	621175
Entrez	51315

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 22 protein_coding

ENST00000347055, ENST00000672766, ENST00000910792, ENST00000910793, ENST00000910794, ENST00000910795, ENST00000910796, ENST00000910797, ENST00000910798, ENST00000912426, ENST00000912427, ENST00000912428, ENST00000953777, ENST00000953778, ENST00000953779, ENST00000953780, ENST00000953781, ENST00000953782, ENST00000953783, ENST00000953784, ENST00000953785, ENST00000953786

RefSeq mRNA: 2 — MANE Select: NM_016618 NM_001304526, NM_016618

CCDS: CCDS2000

Canonical transcript exons

ENST00000347055 — 4 exons

Exon	Start	End
ENSE00001144361	88027205	88028585
ENSE00001158553	88034134	88034292
ENSE00001158563	88036943	88037051
ENSE00001390640	88055626	88055783

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 96.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.6295 / max 151.7367, expressed in 1789 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29588	11.1210	1760
29587	1.6902	1013
29589	0.8414	551
29590	0.8347	511
202276	0.1423	41

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic mucosa	UBERON:0000317	96.84	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.73	gold quality
epithelium of nasopharynx	UBERON:0001951	96.06	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.82	gold quality
skin of hip	UBERON:0001554	95.72	gold quality
bronchial epithelial cell	CL:0002328	95.49	gold quality
calcaneal tendon	UBERON:0003701	95.29	gold quality
jejunal mucosa	UBERON:0000399	94.98	gold quality
rectum	UBERON:0001052	94.96	gold quality
upper leg skin	UBERON:0004262	94.96	gold quality
caput epididymis	UBERON:0004358	94.55	gold quality
seminal vesicle	UBERON:0000998	94.41	gold quality
corpus epididymis	UBERON:0004359	94.29	gold quality
oral cavity	UBERON:0000167	94.28	gold quality
lower esophagus mucosa	UBERON:0035834	94.20	gold quality
endometrium	UBERON:0001295	94.17	gold quality
palpebral conjunctiva	UBERON:0001812	94.10	gold quality
choroid plexus epithelium	UBERON:0003911	93.94	gold quality
tendon	UBERON:0000043	93.74	gold quality
mucosa of transverse colon	UBERON:0004991	93.67	gold quality
urethra	UBERON:0000057	93.56	gold quality
epithelium of bronchus	UBERON:0002031	93.48	gold quality
mammary duct	UBERON:0001765	93.42	gold quality
bronchus	UBERON:0002185	93.34	gold quality
germinal epithelium of ovary	UBERON:0001304	93.33	gold quality
jejunum	UBERON:0002115	93.28	gold quality
parotid gland	UBERON:0001831	93.22	gold quality
trabecular bone tissue	UBERON:0002483	93.10	gold quality
epithelium of mammary gland	UBERON:0003244	93.10	gold quality
ileal mucosa	UBERON:0000331	93.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting KRCC1, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-379-3P	99.69	69.60	1524
HSA-MIR-411-3P	99.69	69.63	1524
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-3915	99.45	68.49	1905

Literature-anchored findings (GeneRIF, showing 2)

• By observing the data obtained from the isothermal titration calorimetry assay, both of the human proteins (KRCC1 and ZFAND6) were demonstrated to bind to their respective Toxoplasma gondii SAG1 and SAG2 proteins. (PMID:29351065)
• KRCC1: A potential therapeutic target in ovarian cancer. (PMID:31908025)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:171482	ENSDARG00000074415
mus_musculus	Krcc1	ENSMUSG00000053012
rattus_norvegicus	Krcc1	ENSRNOG00000007124
drosophila_melanogaster	CG1231	FBGN0035134
drosophila_melanogaster	dbf	FBGN0287630

Paralogs (9): ZNF346 (ENSG00000113761), ZNF385B (ENSG00000144331), ZMAT2 (ENSG00000146007), ZNF385D (ENSG00000151789), ZNF385A (ENSG00000161642), ZMAT4 (ENSG00000165061), ZMAT1 (ENSG00000166432), ZMAT3 (ENSG00000172667), ZNF385C (ENSG00000187595)

Protein

Protein identifiers

Lysine-rich coiled-coil protein 1 — Q9NPI7 (reviewed: Q9NPI7)

Alternative names: Cryptogenic hepatitis-binding protein 2, HLY

All UniProt accessions (1): Q9NPI7

UniProt curated annotations — full annotation on UniProt →

Function. Regulates CHEK1-mediated cell cycle checkpoint. Facilitates efficient recombination and homologous recombination repair. Required for proper S-phase progression and mitotic entry.

Subunit / interactions. Interacts with CHEK1; the interaction promotes CHEK1 phosphorylation at ‘Ser-296’. (Microbial infection) Interacts with Toxoplasma gondii SAG1.

Subcellular location. Nucleus.

RefSeq proteins (2): NP_001291455, NP_057702* (*=MANE)

Domains & families (InterPro)

UniProt features (7 total): compositionally biased region 4, chain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NPI7-F1	58.49	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 103 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, TTGGGAG_MIR150, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, MAF_Q6, RYTTCCTG_ETS2_B, chr2p11, BASAKI_YBX1_TARGETS_DN, EGR1_01, HAN_SATB1_TARGETS_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, CHEN_HOXA5_TARGETS_9HR_UP, E2F1_Q3_01

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

180 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRCC1	CPSF4L	A6NMK7	493
KRCC1	HEBP1	Q9NRV9	448
KRCC1	CCNL1	Q9UK58	444
KRCC1	THNSL2	Q86YJ6	419
KRCC1	ZNF644	Q9H582	419
KRCC1	TMEM101	Q96IK0	412
KRCC1	SPMIP9	Q96LM6	405
KRCC1	ANGEL2	Q5VTE6	401
KRCC1	MLC1	Q15049	400
KRCC1	FOXI3	A8MTJ6	400
KRCC1	SANBR	Q6NSI8	397
KRCC1	MRPL35	Q9NZE8	394
KRCC1	PLAC8	Q9NZF1	371
KRCC1	SLX9	Q9NSI2	370
KRCC1	PPP1CC	P36873	359

IntAct

17 interactions, top by confidence:

A	B	Type	Score
NKAPD1	KRCC1	psi-mi:“MI:0915”(physical association)	0.560
ARL6IP4	KRCC1	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	KRCC1	psi-mi:“MI:0915”(physical association)	0.560
KRCC1	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
KRCC1	GTF2IRD1	psi-mi:“MI:0915”(physical association)	0.400
KRCC1	PPP1CC	psi-mi:“MI:0915”(physical association)	0.370
GAMMAHV.ORF63	KRCC1	psi-mi:“MI:0915”(physical association)	0.370
SPANXN2	KRCC1	psi-mi:“MI:0915”(physical association)	0.000
NKAPD1	KRCC1	psi-mi:“MI:0915”(physical association)	0.000
ARL6IP4	KRCC1	psi-mi:“MI:0915”(physical association)	0.000
bipA	KRCC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (9): KRCC1 (Affinity Capture-RNA), KRCC1 (Two-hybrid), ARL6IP4 (Two-hybrid), SPANXN2 (Two-hybrid), GTF2IRD1 (Affinity Capture-MS), KRCC1 (Affinity Capture-MS), KRCC1 (Affinity Capture-RNA), KRCC1 (Affinity Capture-RNA), KRCC1 (Two-hybrid)

ESM2 similar proteins: A0A140LFM6, A0A1B0GVH6, A1A4G5, A1CQN6, A7A241, A9RNY0, B0QZF7, B9UYK6, E9Q309, H0WFA5, O23372, O35413, O94875, P02686, P43587, Q0VFP3, Q0WL69, Q12912, Q17QQ9, Q1G3K8, Q32KY7, Q3UTJ2, Q499E5, Q4R309, Q4R881, Q4V7T5, Q56WM6, Q5E9A0, Q5PPL1, Q5R6I3, Q5VT06, Q62417, Q6AYU0, Q6DD19, Q6GP48, Q6H7U2, Q8K2H1, Q8L4M6, Q8NEY8, Q8NG27

Diamond homologs: Q17QQ9, Q28EG9, Q3V0C1, Q5H9K5, Q5PPL1, Q5R6I3, Q99JT5, Q9NPI7, A2RV29, B0JZ85, O08781, O54836, Q0IIC4, Q0VD35, Q5R4W8, Q8AVN9, Q8BZ94, Q9H898, Q9HA38, Q9R0B7, Q9UL40, A0A096LPI5, A6NJG6, F2Z398, Q09FC8, Q68CZ1, Q8IV13, Q8N9N2, Q8TDM0, Q92918, Q96J02, Q96MD7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	32
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1176758	GRCh37/hg19 2p11.2(chr2:88007281-90260248)x1	Pathogenic

SpliceAI

858 predictions. Top by Δscore:

Variant	Effect	Δscore
2:88028582:TTTT:T	acceptor_gain	0.9900
2:88028584:TT:T	acceptor_gain	0.9900
2:88028586:C:CC	acceptor_gain	0.9900
2:88034132:AC:A	donor_gain	0.9900
2:88034133:CC:C	donor_gain	0.9900
2:88036936:AACCT:A	donor_loss	0.9900
2:88036937:ACCTA:A	donor_loss	0.9900
2:88036938:CCT:C	donor_loss	0.9900
2:88036939:CT:C	donor_loss	0.9900
2:88036940:TA:T	donor_loss	0.9900
2:88036941:ACCT:A	donor_loss	0.9900
2:88036942:C:CA	donor_loss	0.9900
2:88055621:CTCA:C	donor_loss	0.9900
2:88055622:TCA:T	donor_loss	0.9900
2:88055623:CACCT:C	donor_loss	0.9900
2:88055624:A:C	donor_loss	0.9900
2:88055625:C:CG	donor_loss	0.9900
2:88055625:CCTT:C	donor_gain	0.9900
2:88028582:TTTTC:T	acceptor_loss	0.9800
2:88028583:TTT:T	acceptor_gain	0.9800
2:88028583:TTTC:T	acceptor_loss	0.9800
2:88028584:TTCTG:T	acceptor_loss	0.9800
2:88028585:TCTG:T	acceptor_loss	0.9800
2:88028587:T:C	acceptor_loss	0.9800
2:88028588:G:C	acceptor_loss	0.9800
2:88029460:C:CT	donor_gain	0.9800
2:88029461:T:TT	donor_gain	0.9800
2:88034290:CAT:C	acceptor_gain	0.9800
2:88038191:A:AC	donor_gain	0.9800
2:88034288:CTCAT:C	acceptor_gain	0.9700

AlphaMissense

1732 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:88027808:C:A	W252C	0.994
2:88027808:C:G	W252C	0.994
2:88028531:A:C	F11L	0.993
2:88028531:A:T	F11L	0.993
2:88028533:A:G	F11L	0.993
2:88027810:A:G	W252R	0.989
2:88027810:A:T	W252R	0.989
2:88028498:C:A	Q22H	0.989
2:88028498:C:G	Q22H	0.989
2:88027787:A:C	F259L	0.986
2:88027787:A:T	F259L	0.986
2:88027789:A:G	F259L	0.986
2:88027801:A:G	S255P	0.983
2:88028489:T:A	R25S	0.980
2:88028489:T:G	R25S	0.980
2:88027809:C:G	W252S	0.979
2:88028465:G:C	F33L	0.977
2:88028465:G:T	F33L	0.977
2:88028467:A:G	F33L	0.977
2:88027797:A:G	I256T	0.975
2:88027797:A:C	I256S	0.974
2:88028520:A:G	L15P	0.974
2:88027797:A:T	I256N	0.972
2:88028520:A:T	L15H	0.970
2:88028532:A:G	F11S	0.970
2:88027792:C:G	G258R	0.965
2:88027792:C:T	G258R	0.965
2:88028532:A:C	F11C	0.961
2:88027812:A:G	L251P	0.959
2:88028494:C:G	A24P	0.959

dbSNP variants (sampled 300 via entrez): RS1000102094 (2:88034875 T>C), RS1000184371 (2:88056286 C>G), RS1000268008 (2:88044857 T>G), RS1000291629 (2:88048841 A>G), RS1000563946 (2:88042152 C>T), RS1000627464 (2:88047344 A>C), RS1000634960 (2:88032272 C>T), RS1000715275 (2:88039458 G>A), RS1000745051 (2:88039666 C>T), RS1000890160 (2:88055069 G>A,C), RS1001015350 (2:88040297 C>T), RS1001175564 (2:88043881 G>A), RS1001253467 (2:88053428 CACG>C), RS1001292102 (2:88038495 G>A), RS1001301155 (2:88050502 A>C,G)

Disease associations

OMIM: gene MIM:621175 | 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
GCST000386_6	Bilirubin levels	5.000000e-07
GCST003542_178	Night sleep phenotypes	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004570	bilirubin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases expression, affects expression	7
sodium arsenite	decreases expression, increases expression	3
Air Pollutants	decreases expression, increases expression, affects expression, increases abundance	3
Estradiol	decreases expression, affects expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
GSK-J4	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	decreases expression	1
titanium dioxide	increases methylation	1
trichostatin A	increases expression	1
arsenite	affects binding, increases reaction	1
sulforaphane	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
ochratoxin A	increases expression	1
ferrous chloride	decreases expression	1
beta-methylcholine	affects expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
bisphenol S	decreases expression	1
PCI 5002	affects cotreatment, increases expression	1
bisphenol AF	decreases expression	1
Decitabine	increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	increases expression	1
Leflunomide	increases expression	1
Air Pollutants, Occupational	decreases expression	1

Clinical trials (associated diseases)

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