CHD1L

chromodomain helicase DNA binding protein 1 like, the group of Macro domain containing

Basic information

Region (hg38): 1:147242653-147295765

Links

ENSG00000131778 ∙ NCBI:9557 ∙ OMIM:613039 ∙ HGNC:1916 ∙ Uniprot:Q86WJ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital anomaly of kidney and urinary tract (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHD1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHD1L gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	9	14
missense			68	6	6	80
nonsense			2	1		3
start loss				1		1
frameshift			3			3
inframe indel						0
splice donor/acceptor (+/-2bp)			1	1		2
splice region				1	7	8
non coding				2	56	58
Total	0	0	74	16	71

Variants in CHD1L

This is a list of pathogenic ClinVar variants found in the CHD1L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-147242704-A-T		CHD1L-related disorder	Likely benign (Sep 08, 2022)
1-147242720-C-G		not specified	Uncertain significance (Apr 18, 2023)
1-147242726-G-T		CHD1L-related disorder	Likely benign (Mar 20, 2020)
1-147242731-G-C		not specified	Uncertain significance (Dec 27, 2023)
1-147242737-C-A		not specified	Uncertain significance (Apr 15, 2024)
1-147242738-A-G		not specified	Uncertain significance (Nov 14, 2023)
1-147242739-A-G		CHD1L-related disorder	Likely benign (Feb 13, 2020)
1-147242742-C-T			Benign (Nov 12, 2018)
1-147242742-C-C			Benign (Nov 10, 2018)
1-147242750-T-A		not specified	Uncertain significance (May 03, 2023)
1-147242777-G-C			Benign (Nov 10, 2018)
1-147242789-C-T		not specified	Uncertain significance (Jun 22, 2024)
1-147242815-C-A		not specified	Uncertain significance (Apr 19, 2024)
1-147242820-G-C		not specified	Uncertain significance (Apr 19, 2024)
1-147242938-T-T			Benign (Nov 10, 2018)
1-147252286-C-T			Benign (Nov 10, 2018)
1-147252348-A-G			Benign (Nov 10, 2018)
1-147252438-G-G			Benign (Nov 10, 2018)
1-147252634-C-T		not specified	Uncertain significance (Apr 09, 2024)
1-147252666-C-T		CHD1L-related disorder	Likely benign (Oct 28, 2019)
1-147252721-G-T		not specified	Uncertain significance (Jan 04, 2024)
1-147252729-C-T		Abnormality of the urinary system	Uncertain significance (-)
1-147252731-G-T		not specified	Uncertain significance (Oct 28, 2023)
1-147252753-G-A			Benign (Nov 10, 2018)
1-147254521-T-C			Benign (Nov 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHD1L	protein_coding	protein_coding	ENST00000369258	23	53153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00e-36	0.00000288	125051	2	695	125748	0.00278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.580	490	455	1.08	0.0000234	5808
Missense in Polyphen		154	151.5	1.0165		1894
Synonymous	-0.0463	167	166	1.00	0.00000830	1696
Loss of Function	-0.239	54	52.1	1.04	0.00000286	622

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00731	0.00715
Ashkenazi Jewish	0.000741	0.000695
East Asian	0.00624	0.00622
Finnish	0.000879	0.000878
European (Non-Finnish)	0.00269	0.00268
Middle Eastern	0.00624	0.00622
South Asian	0.00255	0.00242
Other	0.00232	0.00228

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA helicase which plays a role in chromatin-remodeling following DNA damage. Targeted to sites of DNA damage through interaction with poly(ADP-ribose) and functions to regulate chromatin during DNA repair. Able to catalyze nucleosome sliding in an ATP-dependent manner. Helicase activity is strongly stimulated upon poly(ADP-ribose)-binding. {ECO:0000269|PubMed:18023026, ECO:0000269|PubMed:19661379}.
• Pathway: DNA Repair;Formation of Incision Complex in GG-NER;Dual Incision in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Nucleotide Excision Repair (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• rvis_EVS: 1.09
• rvis_percentile_EVS: 91.91

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.575
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Chd1l

Gene ontology

• Biological process: DNA repair;nucleotide-excision repair, preincision complex stabilization;nucleotide-excision repair, preincision complex assembly;nucleotide-excision repair, DNA incision, 5'-to lesion;chromatin remodeling;cellular response to DNA damage stimulus;DNA duplex unwinding;nucleotide-excision repair, DNA incision;global genome nucleotide-excision repair
• Cellular component: nucleus;nucleoplasm;cytosol;plasma membrane
• Molecular function: nucleotide binding;ATP-dependent DNA helicase activity;protein binding;ATP binding;ATPase activity