ATRX

Chr X

ATRX chromatin remodeler

Involved in transcriptional regulation and chromatin remodeling. Facilitates DNA replication in multiple cellular environments and is required for efficient replication of a subset of genomic loci. Binds to DNA tandem repeat sequences in both telomeres and euchromatin and in vitro binds DNA quadruplex structures. May help stabilizing G-rich regions into regular chromatin structures by remodeling G4 DNA and incorporating H3.3-containing nucleosomes. Catalytic component of the chromatin remodeling complex ATRX:DAXX which has ATP-dependent DNA translocase activity and catalyzes the replication-independent deposition of histone H3.3 in pericentric DNA repeats outside S-phase and telomeres, and the in vitro remodeling of H3.3-containing nucleosomes. Its heterochromatin targeting is proposed to involve a combinatorial readout of histone H3 modifications (specifically methylation states of H3K9 and H3K4) and association with CBX5. Involved in maintaining telomere structural integrity in embryonic stem cells which probably implies recruitment of CBX5 to telomeres. Reports on the involvement in transcriptional regulation of telomeric repeat-containing RNA (TERRA) are conflicting; according to a report, it is not sufficient to decrease chromatin condensation at telomeres nor to increase expression of telomeric RNA in fibroblasts (PubMed:24500201). May be involved in telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines. Acts as a negative regulator of chromatin incorporation of transcriptionally repressive histone MACROH2A1, particularily at telomeres and the alpha-globin cluster in erythroleukemic cells. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, required for the chromatin occupancy of SMC1 and CTCF within the H19 imprinting control region (ICR) and involved in establishment of histone tails modifications in the ICR. May be involved in brain development and facial morphogenesis. Binds to zinc-finger coding genes with atypical chromatin signatures and regulates its H3K9me3 levels. Forms a complex with ZNF274, TRIM28 and SETDB1 to facilitate the deposition and maintenance of H3K9me3 at the 3' exons of zinc-finger genes (PubMed:27029610)

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtAlpha-thalassemia/impaired intellectual development syndrome, X-linked
UniProtIntellectual disability-hypotonic facies syndrome, X-linked, 1
UniProtAlpha-thalassemia myelodysplasia syndrome

Clinical highlights

Gene-disease validity (ClinGen)
ATR-X-related syndrome · XLDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
5
Active trials
343
Pubs (1 yr)
P/LP submissions
P/LP missense
0.12
LOEUF· LoF intol.
LOF
Mechanism· G2P
Some data sources returned errors (2)

ncbi: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint?
0.12LOEUF
pLI 1.000
Z-score 8.22
OE 0.06 (0.030.12)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
3.10Z-score
OE missense 0.70 (0.660.75)
604 obs / 860.0 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.06 (0.030.12)
00.351.4
Missense OE?0.70 (0.660.75)
00.61.4
Synonymous OE?1.06
01.21.6
LoF obs/exp: 5 / 88.5Missense obs/exp: 604 / 860.0Syn Z: -0.82

ClinVar

No ClinVar data available.

Protein Context — Lollipop Plot

ATRX · protein map & ClinVar variants

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