CHD1L

Chr 1

chromodomain helicase DNA binding protein 1 like

Also known as: ALC1, CHDL

NCBI Gene: 9557 ENSG00000131778 UniProt: Q86WJ1 OMIM: 613039

This gene encodes an ATP-dependent chromatin remodeler that recognizes poly-ADP-ribosylated histones at DNA damage sites and catalyzes nucleosome sliding to facilitate DNA repair. Mutations cause autosomal dominant intellectual disability with epilepsy and characteristic dysmorphic features, typically presenting in early childhood. The gene is not highly constrained against loss-of-function variants, and clinical presentations can include developmental delay, seizures, and craniofacial abnormalities.

GeneReviews OMIM ResearchSummary from RefSeq, UniProt

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]

GeneReviews OMIM ResearchGenerating clinical summary…

LOEUF 1.30

Clinical Summary— CHD1L

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Gene-Disease Validity (ClinGen)

congenital anomaly of kidney and urinary tract · ADLimited

Limited evidence — not for standalone diagnostic reporting

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

236 VUS of 394 total submissions

Explore recent and relevant literature in Research Assistant →

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GeneReview available — CHD1L

Authoritative clinical overview · Recommended first read

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

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?

-0.58Z-score

OE missense 1.08 (1.00–1.16)

490 obs / 455.2 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.04 (0.83–1.30)

0≤0.351.4

Missense OE?1.08 (1.00–1.16)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 54 / 52.1Missense obs/exp: 490 / 455.2Syn Z: -0.05

ClinVar Variant Classifications

394 submitted variants in ClinVar

ClinVar

Classification Summary

VUS236

Likely Benign32

Benign85

Conflicting1

236

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	6	230	0	0	236
Likely Benign	2	15	4	11	32
Benign	0	7	68	10	85
Conflicting	—				1
Total	8	252	72	21	354

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

View in ClinVar →

289 pathogenic / likely-pathogenic (of 306) ClinVar copy-number / structural variants overlap CHD1L — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →