CHCT1

Summary

CHCT1 (CHD1 helical C-terminal domain containing 1, HGNC:26990) is a protein-coding gene on chromosome 17q23.2, encoding CHD1 helical C-terminal domain containing protein 1 (Q86WR6). May play a role in regulation of apoptosis.

Located in nucleus.

Source: NCBI Gene 124773 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_181707

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26990
Approved symbol	CHCT1
Name	CHD1 helical C-terminal domain containing 1
Location	17q23.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000141371
Ensembl biotype	protein_coding
Entrez	124773

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000269127, ENST00000461535, ENST00000464714, ENST00000474834

RefSeq mRNA: 1 — MANE Select: NM_181707 NM_181707

CCDS: CCDS32698

Canonical transcript exons

ENST00000269127 — 6 exons

Exon	Start	End
ENSE00001046249	60429362	60429557
ENSE00001899543	60422489	60422643
ENSE00001913680	60431181	60431426
ENSE00002917172	60426161	60426336
ENSE00003301692	60426718	60426817
ENSE00003625256	60425783	60425884

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 97.60.

FANTOM5 (CAGE): breadth broad, TPM avg 2.3528 / max 232.7599, expressed in 414 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
162045	0.8235	196
162043	0.7646	192
162044	0.5241	154
162047	0.1374	5
162048	0.0547	3
162046	0.0485	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	97.60	gold quality
right testis	UBERON:0004534	97.40	gold quality
testis	UBERON:0000473	95.18	gold quality
adult organism	UBERON:0007023	90.96	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.67	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.90	gold quality
buccal mucosa cell	CL:0002336	74.85	gold quality
sperm	CL:0000019	70.83	gold quality
granulocyte	CL:0000094	63.71	gold quality
tendon of biceps brachii	UBERON:0008188	57.93	silver quality
vena cava	UBERON:0004087	56.96	gold quality
trabecular bone tissue	UBERON:0002483	56.88	gold quality
upper leg skin	UBERON:0004262	56.12	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	55.57	gold quality
cerebellar vermis	UBERON:0004720	51.73	gold quality
monocyte	CL:0000576	49.22	gold quality
leukocyte	CL:0000738	48.78	gold quality
subcutaneous adipose tissue	UBERON:0002190	46.98	gold quality
saphenous vein	UBERON:0007318	46.81	gold quality
mammalian vulva	UBERON:0000997	46.52	gold quality
metanephros cortex	UBERON:0010533	46.39	gold quality
biceps brachii	UBERON:0001507	45.72	gold quality
amniotic fluid	UBERON:0000173	45.00	gold quality
nipple	UBERON:0002030	44.97	gold quality
spleen	UBERON:0002106	44.62	gold quality
metanephros	UBERON:0000081	44.53	gold quality
adipose tissue	UBERON:0001013	44.39	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
pharyngeal mucosa	UBERON:0000355	43.29	gold quality
blood	UBERON:0000178	43.22	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	29.17
E-ANND-3	no	2.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting CHCT1, 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-8080	99.82	67.52	1342
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-3161	98.71	67.14	816
HSA-MIR-4646-3P	98.65	66.98	693
HSA-MIR-6831-5P	98.26	67.20	990
HSA-MIR-3927-3P	97.68	66.76	892
HSA-MIR-1224-3P	97.24	65.92	851
HSA-MIR-215-3P	97.02	68.01	1209
HSA-MIR-4433B-5P	95.91	66.56	727

Literature-anchored findings (GeneRIF, showing 1)

• Expression profile analysis of a new testis-specifically expressed gene C17ORF64 and its association with cell apoptosis in MCF-7 cells. (PMID:33566224)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Chct1	ENSMUSG00000018479
rattus_norvegicus	Chct1	ENSRNOG00000003143

Protein

Protein identifiers

CHD1 helical C-terminal domain containing protein 1 — Q86WR6 (reviewed: Q86WR6)

All UniProt accessions (3): A0A0G2JLI9, K7EQ24, Q86WR6

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in regulation of apoptosis.

Subcellular location. Cytoplasm. Nucleus.

Domain organisation. The CHD1 helical C-terminal domain (CHCT) may bind DNA and nucleosomes.

RefSeq proteins (1): NP_859058* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025260	CHD1-like_C	Domain
IPR039880	CHCT1-like	Family

Pfam: PF13907

UniProt features (4 total): region of interest 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86WR6-F1	69.32	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 61 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER, chr17q23, SRC_UP.V1_DN, CBX5_TARGET_GENES, DACH1_TARGET_GENES, FOXG1_TARGET_GENES, HMG20B_TARGET_GENES, KLF7_TARGET_GENES, NAB2_TARGET_GENES, RBM34_TARGET_GENES, SETD7_TARGET_GENES, TFEB_TARGET_GENES, ZBTB18_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1861 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHCT1	CDRT15L2	A8MXV6	583
CHCT1	DEFB123	Q8N688	571
CHCT1	APPBP2	Q92624	555
CHCT1	INTS2	Q9H0H0	546
CHCT1	USP32	Q8NFA0	518
CHCT1	RNFT1	Q5M7Z0	508
CHCT1	TBC1D28	Q2M2D7	507
CHCT1	CCDC144A	A2RUR9	496
CHCT1	HEATR6	Q6AI08	483
CHCT1	SLC35G6	P0C7Q6	480
CHCT1	SLC35G3	Q8N808	480
CHCT1	DHX40	Q8IX18	474
CHCT1	SPDYE4	A6NLX3	474
CHCT1	OR3A2	P47893	474
CHCT1	IRX2	Q9BZI1	462

IntAct

0 interactions, top by confidence:

BioGRID (1): C17orf64 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTR0, A0A1B0GTY4, A0A1B0GVD1, A7WNB0, A8R0V4, E9Q7F5, O55779, O70552, O75818, O93036, P01586, P03212, P03319, P03321, P04823, P0DOE0, P10260, P13206, P16837, P20880, P28907, P36340, P47939, P47940, Q02484, Q03233, Q1HVF6, Q2HRD2, Q3KSS3, Q3TTJ4, Q5BK38, Q5QR91, Q5VAN0, Q64277, Q66669, Q66672, Q6GQU0, Q6GVM5, Q6UWF9, Q86WR6

Diamond homologs: A9X4T1, B6ZLK2, E9PZM4, O14646, O14647, P40201, Q32KP7, Q7KU24, Q86WR6, Q9D979

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1065 predictions. Top by Δscore:

Variant	Effect	Δscore
17:60425778:CCTAG:C	acceptor_loss	1.0000
17:60425779:CTA:C	acceptor_loss	1.0000
17:60425780:TA:T	acceptor_loss	1.0000
17:60425781:A:C	acceptor_loss	1.0000
17:60425880:AAACT:A	donor_gain	1.0000
17:60425881:AACT:A	donor_gain	1.0000
17:60425882:ACT:A	donor_gain	1.0000
17:60425882:ACTGT:A	donor_loss	1.0000
17:60425883:CT:C	donor_gain	1.0000
17:60425883:CTG:C	donor_loss	1.0000
17:60425885:G:GG	donor_gain	1.0000
17:60425886:T:A	donor_loss	1.0000
17:60426241:G:GT	donor_gain	1.0000
17:60426333:GAAA:G	donor_gain	1.0000
17:60426337:G:GG	donor_gain	1.0000
17:60426849:C:G	donor_gain	1.0000
17:60429341:AACAC:A	acceptor_gain	1.0000
17:60429555:AAGG:A	donor_loss	1.0000
17:60429556:AGGTA:A	donor_loss	1.0000
17:60429557:GGTAA:G	donor_loss	1.0000
17:60429558:G:GA	donor_loss	1.0000
17:60425781:A:AG	acceptor_gain	0.9900
17:60425782:G:GG	acceptor_gain	0.9900
17:60425782:GGT:G	acceptor_gain	0.9900
17:60425887:G:GT	donor_loss	0.9900
17:60425888:A:AG	donor_gain	0.9900
17:60425888:AGT:A	donor_loss	0.9900
17:60425889:G:GG	donor_gain	0.9900
17:60426130:T:TA	acceptor_gain	0.9900
17:60426159:A:AG	acceptor_gain	0.9900

AlphaMissense

1551 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:60426731:T:C	F115L	0.990
17:60426733:C:A	F115L	0.990
17:60426733:C:G	F115L	0.990
17:60426743:T:C	F119L	0.989
17:60426745:C:A	F119L	0.989
17:60426745:C:G	F119L	0.989
17:60426166:A:C	K53N	0.988
17:60426166:A:T	K53N	0.988
17:60426165:A:T	K53I	0.979
17:60426725:T:A	W113R	0.978
17:60426725:T:C	W113R	0.978
17:60425876:T:C	F49L	0.970
17:60425878:C:A	F49L	0.970
17:60425878:C:G	F49L	0.970
17:60426187:G:C	K60N	0.966
17:60426187:G:T	K60N	0.966
17:60426290:T:C	F95L	0.965
17:60426292:T:A	F95L	0.965
17:60426292:T:G	F95L	0.965
17:60426727:G:C	W113C	0.960
17:60426727:G:T	W113C	0.960
17:60426257:A:C	S84R	0.957
17:60426259:C:A	S84R	0.957
17:60426259:C:G	S84R	0.957
17:60426204:T:C	L66S	0.954
17:60426732:T:C	F115S	0.952
17:60426273:G:T	G89V	0.950
17:60426191:T:C	F62L	0.947
17:60426193:C:A	F62L	0.947
17:60426193:C:G	F62L	0.947

dbSNP variants (sampled 300 via entrez): RS1000013402 (17:60420196 G>T), RS1000358498 (17:60420087 TATTTTA>T), RS1000468956 (17:60426367 A>G), RS1000585884 (17:60422137 C>T), RS1000691460 (17:60421725 GACTACA>G), RS1001113673 (17:60427479 G>A), RS1001194093 (17:60430700 C>G,T), RS1001357327 (17:60425387 T>C), RS1001422462 (17:60424925 T>G), RS1001459662 (17:60421829 G>A), RS1001546945 (17:60424978 A>G), RS1001873731 (17:60425129 C>G), RS1003229333 (17:60423601 T>C), RS1003294243 (17:60429259 G>A,C,T), RS1003420616 (17:60423867 A>C,G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium	decreases expression, increases abundance	2
Resveratrol	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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