CHD1L
Basic information
Region (hg38): 1:147242654-147295765
Links
Phenotypes
GenCC
Source:
- congenital anomaly of kidney and urinary tract (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (120 variants)
- not_provided (49 variants)
- CHD1L-related_disorder (24 variants)
- Congenital_anomaly_of_kidney_and_urinary_tract (3 variants)
- Short_stature (1 variants)
- Abnormality_of_the_urinary_system (1 variants)
- Hereditary_breast_ovarian_cancer_syndrome (1 variants)
- Decreased_total_neutrophil_count (1 variants)
- Decreased_total_lymphocyte_count (1 variants)
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. These statistics are base on transcript: NM_000004284.6. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 16 | |||||
missense | 128 | 11 | 142 | |||
nonsense | 3 | |||||
start loss | 1 | 1 | ||||
frameshift | 3 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
Total | 0 | 0 | 135 | 23 | 9 |
GnomAD
Source:
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:
- 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
- loftool
- 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
- Phenotype
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