CHD1L (chromodomain helicase DNA binding protein 1 like)

Gene

• Entrez ID: 9557
• Gene name: Chromodomain helicase DNA binding protein 1 like
• Gene symbol: CHD1L
• Synonyms (NCBI Gene): ALC1, CHDL
• Chromosome: 1
• Chromosome location: 1q21.1
• Summary: This gene encodes a DNA helicase protein involved in DNA repair. The protein converts ATP to add poly(ADP-ribose) as it regulates chromatin relaxation following DNA damage. Overexpression of this gene has been linked to several types of cancers. [provided

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs782144677	A>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT044802	hsa-miR-320a	CLASH	23622248
MIRT1963410	hsa-miR-326	CLIP-seq
MIRT1963411	hsa-miR-330-5p	CLIP-seq
MIRT1963412	hsa-miR-555	CLIP-seq
MIRT2199871	hsa-miR-5095	CLIP-seq
MIRT2199872	hsa-miR-552	CLIP-seq
MIRT2199873	hsa-miR-656	CLIP-seq
MIRT2502570	hsa-miR-203	CLIP-seq
MIRT2502571	hsa-miR-25	CLIP-seq
MIRT2502572	hsa-miR-32	CLIP-seq
MIRT2502573	hsa-miR-363	CLIP-seq
MIRT2502574	hsa-miR-367	CLIP-seq
MIRT2502575	hsa-miR-4303	CLIP-seq
MIRT2502576	hsa-miR-4311	CLIP-seq
MIRT2502577	hsa-miR-4649-3p	CLIP-seq
MIRT2502578	hsa-miR-4738-3p	CLIP-seq
MIRT2502579	hsa-miR-4762-3p	CLIP-seq
MIRT2502580	hsa-miR-92a	CLIP-seq
MIRT2502581	hsa-miR-92b	CLIP-seq
MIRT2502570	hsa-miR-203	CLIP-seq
MIRT2502575	hsa-miR-4303	CLIP-seq
MIRT2502576	hsa-miR-4311	CLIP-seq
MIRT2502578	hsa-miR-4738-3p	CLIP-seq
MIRT2502579	hsa-miR-4762-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IBA
GO:0000166	Function	Nucleotide binding	IDA	19661379
GO:0000166	Function	Nucleotide binding	IEA
GO:0003678	Function	DNA helicase activity	IEA
GO:0003678	Function	DNA helicase activity	TAS	19661379
GO:0005515	Function	Protein binding	IPI	19661379, 19666485, 23891004
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	19661379
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0006281	Process	DNA repair	IDA	34486521
GO:0006281	Process	DNA repair	IDA	34486521
GO:0006281	Process	DNA repair	IEA
GO:0006281	Process	DNA repair	TAS	19661379
GO:0006338	Process	Chromatin remodeling	IBA
GO:0006338	Process	Chromatin remodeling	IDA	19661379
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006974	Process	DNA damage response	IBA
GO:0006974	Process	DNA damage response	IDA	19661379, 29220652, 29220653
GO:0006974	Process	DNA damage response	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IMP	19661379
GO:0031491	Function	Nucleosome binding	IDA	33357431, 34210977, 34486521
GO:0035861	Component	Site of double-strand break	IDA	29220652, 29220653
GO:0090734	Component	Site of DNA damage	IDA	34486521
GO:0140566	Function	Histone reader activity	IDA	34874266
GO:0140658	Function	ATP-dependent chromatin remodeler activity	IDA	29220652, 29220653, 33357431, 34210977, 34486521
GO:0160004	Function	Poly-ADP-D-ribose modification-dependent protein binding	IDA	29220652, 29220653, 34486521, 34874266

Other IDs

• MIM: 613039
• HGNC: 1916
• e!Ensembl: ENSG00000131778

Protein

• UniProt ID: Q86WJ1
• Protein name: Chromodomain-helicase-DNA-binding protein 1-like (EC 3.6.4.-) (Amplified in liver cancer protein 1)
• Protein function: ATP-dependent chromatin remodeler that mediates chromatin-remodeling following DNA damage (PubMed:19661379, PubMed:29220652, PubMed:29220653, PubMed:33357431, PubMed:34210977, PubMed:34486521, PubMed:34874266). Recruited to DNA damage sites thro
• PDB: 6ZHX, 6ZHY, 7ENN, 7EPU, 7OTQ, 8B0A
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00176	SNF2_N	57 → 328	SNF2 family N-terminal domain	Family
  PF00271	Helicase_C	347 → 459	Helicase conserved C-terminal domain	Family

• Tissue specificity: TISSUE SPECIFICITY: Frequently overexpressed in hepatomacellular carcinomas. {ECO:0000269|PubMed:18023026}.
• Sequence:

  MERAGATSRGGQAPGFLLRLHTEGRAEAARVQEQDLRQWGLTGIHLRSYQLEGVNWLAQR
  FHCQNGCILGDEMGLGKTCQTIALFIYLAGRLNDEGPFLILCPLSVLSNWKEEMQRFAPG
  LSCVTYAGDKEERACLQQDLKQESRFHVLLTTYEICLKDASFLKSFPWSVLVVDEAHRLK
  NQSSLLHKTLSEFSVVFSLLLTGTPIQNSLQELYSLLSFVEPDLFSKEEVGDFIQRYQDI
  EKESESASELHKLLQPFLLRRVKAEVATELPKKTEVVIYHGMSALQKKYYKAILMKDLDA
  FENETAKKVKLQNILSQLRKCVDHPYLFDGVEPEPFEVGDHLTEASGKLHLLDKLLAFLY
  SGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQQPIFVFLLS
  TRAGGVGMNLTAADTVIFVDSDFNPQNDLQAAARAHRIGQNKSVKVIRLIGRDTVEEIVY
  RKAASKLQLTNMIIEGGHFTLGAQKPAADADLQLSEILKFGLDKLLASEGSTMDEIDLES
  ILGETKDGQWVSDALPAAEGGSRDQEEGKNHMYLFEGKDYSKEPSKEDRKSFEQLVNLQK
  TLLEKASQEGRSLRNKGSVLIPGLVEGSTKRKRVLSPEELEDRQKKRQEAAAKRRRLIEE
  KKRQKEEAEHKKKMAWWESNNYQSFCLPSEESEPEDLENGEESSAELDYQDPDATSLKYV
  SGDVTHPQAGAEDALIVHCVDDSGHWGRGGLFTALEKRSAEPRKIYELAGKMKDLSLGGV
  LLFPVDDKESRNKGQDLLALIVAQHRDRSNVLSGIKMAALEEGLKKIFLAAKKKKASVHL
  PRIGHATKGFNWYGTERLIRKHLAARGIPTYIYYFPRSKSAVLHSQSSSSSSRQLVP

• Sequence length: 897

Pathways

Reactome:

Formation of Incision Complex in GG-NER
Dual Incision in GG-NER

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Abnormality of the urinary system	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CAKUT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHD1L-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital anomaly of kidney and urinary tract	Uncertain significance	ClinVar ClinGen, GenCC	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Decreased total lymphocyte count	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Decreased total neutrophil count	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary breast ovarian cancer syndrome	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Short stature	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	BEFREE	26360781		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	26360781		★☆☆☆☆ Found in Text Mining only
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	28332277	Associate	★☆☆☆☆ Found in Text Mining only
Bilateral renal dysplasia	Bilateral renal dysplasia	BEFREE	31759543		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	25153161, 26599012, 30972184, 31322269		★☆☆☆☆ Found in Text Mining only
Breast Diseases	Breast disease	Pubtator	33275888	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	25153161, 33462394, 39201277	Associate	★☆☆☆☆ Found in Text Mining only
Cakut	Congenital anomalies of kidney and urinary tract	BEFREE	22146311		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cakut	Congenital anomalies of kidney and urinary tract	CLINGEN_DG	22146311, 24429398		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cakut	Congenital anomalies of kidney and urinary tract	GENOMICS_ENGLAND_DG	22146311, 24429398		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cakut	Congenital anomalies of the kidney and urinary tract	Pubtator	24429398	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinogenesis	Carcinogenesis	Pubtator	23807680	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	19666485, 23020525, 25153161, 26360781, 32922205, 37923899	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Ovarian Epithelial	Epithelial ovarian carcinoma	Pubtator	32922205	Associate	★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	BEFREE	30127888		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholecystolithiasis	Cholecystolithiasis	BEFREE	30127888		★☆☆☆☆ Found in Text Mining only
Cholelithiasis	Cholelithiasis	BEFREE	30127888		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	23746766		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	28791382, 34045552	Associate	★☆☆☆☆ Found in Text Mining only
Congenital anomaly of the kidney	Multicystic renal dysplasia	BEFREE	22146311		★☆☆☆☆ Found in Text Mining only
Congenital chromosomal disease	Congenital Chromosomal Disease	BEFREE	29408941		★☆☆☆☆ Found in Text Mining only
Congenital heart disease	Congenital Heart Disease	BEFREE	16106982		★☆☆☆☆ Found in Text Mining only
Coronary Arteriosclerosis	Coronary Arteriosclerosis	BEFREE	213762		★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	BEFREE	213762		★☆☆☆☆ Found in Text Mining only
Coronary heart disease	Coronary Heart Disease	BEFREE	213762		★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	29088777, 31340168		★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	BEFREE	31340168		★☆☆☆☆ Found in Text Mining only
Essential Hypertension	Hypertension	Pubtator	35001835	Stimulate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	26162969	Associate	★☆☆☆☆ Found in Text Mining only
Heart Defects Congenital	Congenital heart defect	Pubtator	22318994	Associate	★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	BEFREE	10440925, 10569205, 16106982		★☆☆☆☆ Found in Text Mining only
Hypertrophic obstructive cardiomyopathy	Hypertrophic cardiomyopathy	BEFREE	10569205, 16106982		★☆☆☆☆ Found in Text Mining only
Intrahepatic Cholangiocarcinoma	Intrahepatic Cholangiocarcinoma	BEFREE	31173252, 31524266		★☆☆☆☆ Found in Text Mining only
Invasive Ductal Breast Carcinoma	Invasive Duct and Lobular Carcinoma	BEFREE	26599012		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	18023026, 19441106, 20335658, 20676120, 21068133, 23022495, 24359616, 25153161, 25575811, 26360781, 28946814, 30718500		★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	33723941	Stimulate	★☆☆☆☆ Found in Text Mining only
Lymphopenia	Lymphopenia	BEFREE	31366546		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	25153161, 26599012, 30972184, 31322269		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of esophagus	Esophagus Neoplasm	BEFREE	31340168		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	30127888		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	28646284		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28946814, 30127888		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	27258734		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	19441106, 20335658, 21068133, 23746766, 25153161, 26360781, 28646284, 30024537, 30127888, 30972184		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	26360781, 30718500		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	23020525, 32922205	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	28646284		★☆☆☆☆ Found in Text Mining only
Senior Loken Syndrome	Senior-loken syndrome	Pubtator	31759543	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	26360781		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	31340168		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	33723941	Associate	★☆☆☆☆ Found in Text Mining only
Tetralogy of Fallot	Tetralogy of Fallot	BEFREE	10440925		★☆☆☆☆ Found in Text Mining only
Thymoma	Thymoma	BEFREE	29645059		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	23807680	Associate	★☆☆☆☆ Found in Text Mining only
Werner Syndrome	Werner syndrome	Pubtator	34311961	Associate	★☆☆☆☆ Found in Text Mining only