# NM_000489.6(ATRX):c.4509A>T (p.Arg1503Ser)

https://sugi.bio/variant/atrx-p-arg1503ser

## Summary

**ATRX p.Arg1503Ser (c.4509A>T)** is classified **Likely pathogenic** in ATRX (ClinVar, Single submitter, 1 submitter; last evaluated 2015-12-09). AlphaMissense: likely pathogenic (0.9994); Absent from gnomAD v4.1.

**At a glance:** Likely pathogenic · review: Single submitter · rsID rs1057517997 · 1 submitter · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the ATRX gene that is considered likely disease-causing, submitted by 1 submitter.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [ATRX](https://sugi.bio/atlas/gene/ATRX/) |
| Protein change (HGVS p.) | p.Arg1503Ser |
| Coding change (HGVS c.) | c.4509A>T |
| MANE Select transcript | [NM_000489](https://www.ncbi.nlm.nih.gov/nuccore/NM_000489) |
| dbSNP | [rs1057517997](https://www.ncbi.nlm.nih.gov/snp/rs1057517997/) |
| Variant type | single nucleotide variant |
| Location | chrX:77652162-77652162 (GRCh38) |
| ClinVar | [VCV372813](https://www.ncbi.nlm.nih.gov/clinvar/variation/372813/) |

**All HGVS expressions:** `LRG_1153:g.139108A>T`, `NC_000023.10:g.76907652T>A`, `NC_000023.11:g.77652162T>A`, `NG_008838.3:g.139108A>T`, `NM_000489.6:c.4509A>T`, `NM_138270.5:c.4395A>T`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.9994) — concordant with the pathogenic call
- REVEL 0.263 (benign-leaning) — differs from AlphaMissense
- SaProt LLR -15.749 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt call this damaging; REVEL does not
- Conservation: phyloP -0.57, GERP -4.67, phastCons 0.024 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- AlphaMissense ranks this among the **top 3%** most-pathogenic-predicted substitutions in ATRX (of 14,685 modeled).
- CADD: **PHRED 16.83**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 0.24** across the covering region of the MANE Select transcript (77,633,676–77,652,277), spanning 18,601 bp — the region is depleted of missense variation. Chi-square p 1.7e-15. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**ATRX** population constraint: ClinGen dosage — haploinsufficiency 3, triplosensitivity 0 (0–3 scale). *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **ATR-X-related syndrome** — Definitive (XL)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 52.40, 6% of residues very-high.

**13 experimental structure(s)** (PDB): [2JM1](https://www.rcsb.org/structure/2JM1), [2LBM](https://www.rcsb.org/structure/2LBM), [2LD1](https://www.rcsb.org/structure/2LD1), [3QL9](https://www.rcsb.org/structure/3QL9), [3QLA](https://www.rcsb.org/structure/3QLA), [3QLC](https://www.rcsb.org/structure/3QLC).

## What this gene does {#gene-function}

*Describes the biological roles of ATRX (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** ATRX's established molecular role includes chromatin binding. In Reactome, ATRX is annotated in disease pathway(s) including **Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations**, **Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations**.

**Disease mechanism (Reactome):** ATRX loss or alteration is curated in [Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations](https://reactome.org/content/detail/R-HSA-9670615), [Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations](https://reactome.org/content/detail/R-HSA-9670613).

### Pathways affected {#pathways}

ATRX participates in **3 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations](https://reactome.org/content/detail/R-HSA-9670615) | curated |
| ⚕ [Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations](https://reactome.org/content/detail/R-HSA-9670613) | curated |
| [Inhibition of DNA recombination at telomere](https://reactome.org/content/detail/R-HSA-9670095) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** chromatin binding, DNA translocase activity, histone binding, histone H3K9me2/3 reader activity, chromo shadow domain binding.

**Biological process:** chromatin organization, nucleosome assembly, chromatin remodeling, subtelomeric heterochromatin formation, positive regulation of transcription by RNA polymerase II, negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric.

## Clinical significance {#significance}

**Likely pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2015-12-09.

**Submitter consensus:** unanimous (1/1 Likely pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Likely pathogenic | criteria provided, single submitter | clinical testing | 2015-12-09 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related ATRX variant pages (same residue, condition, or type): [ATRX c.134-2A>G](/variant/atrx-c-134-minus-2a-g), [ATRX c.5449-7A>G](/variant/atrx-c-5449-minus-7a-g), [ATRX p.Arg1022Ter](/variant/atrx-p-arg1022ter), [ATRX p.Arg1661Cys](/variant/atrx-p-arg1661cys), [ATRX p.Arg2085Cys](/variant/atrx-p-arg2085cys), [ATRX p.Arg2085His](/variant/atrx-p-arg2085his), [ATRX p.Arg2131Gln](/variant/atrx-p-arg2131gln), [ATRX p.Arg2178Trp](/variant/atrx-p-arg2178trp).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 372813). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*