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ATRX
Final classification
Unclassified
ATRX c.4434_4435del · p.Lys1479AsnfsTer6
ATRX

NM_000489.5:c.4434_4435del (p.Lys1479AsnfsTer6) is a frameshift deletion in exon 15 of the ATRX gene, predicted to trigger nonsense-mediated decay and result in complete loss of the C-terminal helicase domain and approximately 1,000 C-terminal amino acids.

Gene
ATRX
Transcript
NM_000489.5
HGVS · transcript:coding
NM_000489.5:c.4434_4435del
Consequence
N/A
exon NC_000023.10
GRCh38
chrX:77652235 TTC>T
GRCh37
chrX:76907725 TTC>T
Classification rationale
PVS1PM1PM2 Unclassified
ATRX c.4434_4435del · exon NC_000023.10

NM_000489.5:c.4434_4435del (p.Lys1479AsnfsTer6) is a frameshift deletion in exon 15 of the ATRX gene, predicted to trigger nonsense-mediated decay and result in complete loss of the C-terminal helicase domain and approximately 1,000 C-terminal amino acids.1 ATRX loss of function is an established disease mechanism for ATR-X syndrome, an X-linked disorder characterized by developmental delay, facial dysmorphism, genital abnormalities, and alpha thalassemia.2 The helicase/ATPase domain (aa ~1205-1863) is a critical functional domain in ATRX, harboring approximately 30% of all disease-associated missense mutations. This frameshift removes the entire helicase domain.3 The variant is absent from all gnomAD populations (v2.1, v4.1, Canada), consistent with rarity in the general population.4 No functional studies, clinical observations, segregation data, or variant-specific publications were identified for this specific variant. Five publications retrieved via OncoKB were reviewed in full text; none mention NM_000489.5:c.4434_4435del. These papers address general ATRX biology including the ADD domain structure, R37X translational rescue, mutation spectrum, and ALT phenotype in PanNETs.5

PVS1 + PM1 + PM2 Unclassified
1 pvs1_generic_frameworkpvs1_variant_assessment
2 pvs1_gene_contextPMID:18409179
3 PMID:18409179PMID:17609377
5 PMID:14592816PMID:15591283PMID:17609377PMID:18409179PMID:21719641
Gene diagram · NM_000489.5 · variants mapped to exon structure
ATRX NM_000489.5
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 17 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PVS1 strong Pathogenic
This frameshift deletion (NM_000489.5:c.4434_4435del, p.Lys1479AsnfsTer6) in exon 15 of 35 is predicted to undergo nonsense-mediated decay. ATRX loss of function is an established germline disease mechanism, supported by ATR-X syndrome and the gene-level PVS1 gate confirming eligibility under PMC6185798. No evidence of translational rescue was found for this specific variant location; known rescue mechanisms (e.g., R37X via downstream initiation) are limited to N-terminal mutations and do not extend to exon 15.
Frameshift deletion in exon 15 of 35 exonspredicted NMD targetATRX loss-of-function mechanism established for germline disease (ATR-X syndrome)
PM1 moderate Pathogenic
This frameshift deletion at p.Lys1479 results in premature termination (p.Lys1479AsnfsTer6) that removes the C-terminal helicase/ATPase domain (aa ~1205-1863), a well-characterized critical functional domain in ATRX. The helicase domain harbors approximately 30% of all disease-associated ATRX missense mutations and is essential for chromatin remodeling activity. The truncation eliminates all helicase motifs along with approximately 1,000 C-terminal residues.
The helicase/ATPase domain is a critical functional domain in ATRXharboring ~30% of disease-associated missense mutations (PMID:18409179)Frameshift truncation at p.1479 removes the entire helicase domain and C-terminal region
PM2 moderate Pathogenic
This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). The allele frequency of 0.0% is well below the PM2 threshold of <0.1% for a gene without a VCEP-specific frequency cutoff.
Absent from gnomAD v2.1 (all populations)Absent from gnomAD v4.1 (all populations)Absent from gnomAD-Canada v1.0
Assessed · not applied
Pathogenic
PS2 No de novo observation reported for this variant in any reviewed source.
PS3 No functional studies directly testing NM_000489.5:c.4434_4435del or a systematically characterized range covering position 1479 were identified.
PS4 This variant is absent from ClinVar and has not been reported in any case-control study or clinical cohort.
PM6 No de novo observation (with confirmed maternity and paternity) has been reported for this variant.
PP1 No segregation data are available.
PP3 SpliceAI predicts no significant splice impact (max delta score = 0.04, well below the 0.2 threshold).
PP4 PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5 This variant is absent from ClinVar.
Benign
BA1 This variant is absent from all gnomAD populations (allele frequency = 0.0%).
BS1 This variant is absent from all gnomAD populations (allele frequency = 0.0%).
BS2 No hemizygous observation of this variant has been reported in unaffected male controls.
BS3 No functional studies demonstrating a neutral or benign effect of this variant exist.
BS4 No segregation data are available to evaluate lack of cosegregation with disease.
BP2 This variant has not been observed in trans with a known pathogenic ATRX variant.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product.
BP5 This variant has not been observed in any individual with an alternative molecular basis for disease.
BP6 This variant is absent from ClinVar.
N/A · 8 PS1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
In progress — evidence not uploaded yet.
SpliceAI screenshot
In silico
In progress — evidence not uploaded yet.
Functional / OncoKB screenshot
Functional Likely Oncogenic
In progress — evidence not uploaded yet.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
In progress — evidence not uploaded yet.
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 5 PMIDs not cited in assessment
14592816 ↗ Acquired somatic ATRX mutations in myelodysplastic syndrome associated with alpha thalassemia (ATMDS) convey a more severe hematologic phenotype than germline ATRX mutations. ONCOKB
15591283 ↗ Attenuation of an amino-terminal premature stop codon mutation in the ATRX gene by an alternative mode of translational initiation. ONCOKB
17609377 ↗ Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX. ONCOKB
18409179 ↗ Mutations in the chromatin-associated protein ATRX. ONCOKB
21719641 ↗ Altered telomeres in tumors with ATRX and DAXX mutations. ONCOKB