CHD1L

Chr 1

chromodomain helicase DNA binding protein 1 like

Also known as: ALC1, CHDL

NCBI Gene: 9557ENSG00000131778UniProt: Q86WJ1

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 by RefSeq, Feb 2017]

458
ClinVar variants
107
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— CHD1L
🧬
Gene-Disease Validity (ClinGen)
congenital anomaly of kidney and urinary tract · ADLimited

Limited evidence — not for standalone diagnostic reporting

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
107 Pathogenic / Likely Pathogenic· 234 VUS of 458 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.30LOEUF
pLI 0.000
Z-score -0.24
OE 1.04 (0.83–1.30)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.58Z-score
OE missense 1.08 (1.00–1.16)
490 obs / 455.2 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.04 (0.83–1.30)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.08 (1.00–1.16)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.00
0≤1.21.6
LoF obs/exp: 54 / 52.1Missense obs/exp: 490 / 455.2Syn Z: -0.05

ClinVar Variant Classifications

458 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic104
Likely Pathogenic3
VUS234
Likely Benign31
Benign85
Conflicting1
104
Pathogenic
3
Likely Pathogenic
234
VUS
31
Likely Benign
85
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
104
0
104
Likely Pathogenic
0
0
3
0
3
VUS
3
219
12
0
234
Likely Benign
1
15
4
11
31
Benign
0
7
68
10
85
Conflicting
—1
Total424119121458

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CHD1L · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
📖
GeneReview available — CHD1L
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
The high expression of CHD1L and its clinical significance in human solid tumors: A meta-analysis.
Zhang L et al.·Medicine (Baltimore)
2021Meta-analysis
Clinical significance of CHD1L in hepatocellular carcinoma and therapeutic potentials of virus-mediated CHD1L depletion.
Chen L et al.·Gut
2011
Disrupted transcriptional networks regulated by CHD1L during neurodevelopment underlie the mirrored neuroanatomical and growth phenotypes of the 1q21.1 copy number variant.
Lemée MV et al.·Nucleic Acids Res
2025
Trio exome sequencing identifies de novo variants in novel candidate genes in 19.62% of CAKUT families.
Merz LM et al.·Genet Med
2025
Identification and functional characteristics of CHD1L gene variants implicated in human Müllerian duct anomalies.
Chen S et al.·Biol Res
2024Functional
Africa-specific human genetic variation near CHD1L associates with HIV-1 load.
McLaren PJ et al.·Nature
2023
CHD1L Regulates Cell Cycle, Apoptosis, and Migration in Glioma.
Sun J et al.·Cell Mol Neurobiol
2016
CHD1L is a novel independent prognostic factor for gastric cancer.
Su Z et al.·Clin Transl Oncol
2014
CHD1L promotes hepatocellular carcinoma progression and metastasis in mice and is associated with these processes in human patients.
Chen L et al.·J Clin Invest
2010Cohort
Design, Synthesis, and Biological Evaluation of the First Inhibitors of Oncogenic CHD1L.
Prigaro BJ et al.·J Med Chem
2022
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools