ATRX (Chromatin remodeler ATRX) variants and mutations
ATRX (also known as Chromatin remodeler ATRX) is a human protein-coding gene encoding a chromatin remodeler protein. A chromatin-remodeling protein involved in transcriptional regulation and DNA replication, including at repetitive regions. Variants can cause ATR-X syndrome. This analysis covers 7,549 ATRX variants and mutations. Of these, 92% have computational variant effect predictions. Disease context includes alpha thalassemia-X-linked intellectual disability syndrome, intellectual disability-hypotonic facies syndrome, X-linked, 1, and alpha-thalassemia-myelodysplastic syndrome. Example ATRX variants include M1V, T2A, and T2S.
Variant analysis overview
- Gene: ATRX
- Protein: Chromatin remodeler ATRX
- UniProt accession: P46100
- Organism: Homo sapiens
- Variants analyzed: 7549
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 7,596 unspecified-consequence records; 86 missense variants; 100 synonymous variants; 5 frameshift variants; 3 in-frame deletions; 2 splice-region variants; 1 stop-gained variants; 13 substitution
- Prediction scores: 6,952 variants have prediction scores (92% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: alpha thalassemia-X-linked intellectual disability syndrome, intellectual disability-hypotonic facies syndrome, X-linked, 1, alpha-thalassemia-myelodysplastic syndrome, alpha thalassemia-intellectual disability syndrome type 1, ATR-X-related syndrome, adrenal cortex carcinoma, leiomyosarcoma, glioblastoma, hereditary disease, pancreatic neuroendocrine tumor, anaplastic astrocytoma, Intellectual disability.
Protein structure and variant hotspots
- Protein features: 3 domains; 1 binding sites; 49 post-translational modification sites.
- Structural context: 1,303 variants have structural context.
- PTM context: 138 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Diseases linked to ATRX
Notable ATRX variants
Examples include M1V, T2A, T2S, A3D, A3T, P5L, P5S, M6I. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1V (p.Met1Val), rs2076735328, ClinGen CA413706641, ClinVar RCV001301768, ESM-1b 0.00, AlphaMissense 0.23, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- T2A (p.Thr2Ala), Ensembl rs2148995200, REVEL 0.25, ESM-1b 0.00
- T2S (p.Thr2Ser), rs1557207634, ClinGen CA413706623, ClinVar RCV003112812, TOPMed rs1557207634, REVEL 0.18, ESM-1b 0.00, Likely benign, Alpha thalassemia-X-linked intellectual disability syndrome
- A3D (p.Ala3Asp), TOPMed rs868952037, gnomAD rs868952037, REVEL 0.33, ESM-1b 0.00, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- A3T (p.Ala3Thr), NCI-TCGA TCGA novel, Ensembl rs2148995161, REVEL 0.25, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- P5L (p.Pro5Leu), Ensembl rs2076734639, ESM-1b 0.00, AlphaMissense 0.43
- P5S (p.Pro5Ser), Ensembl rs2148995088, REVEL 0.24, ESM-1b 0.00
- M6I (p.Met6Ile), rs2076734106, ClinGen CA413706567, ClinVar RCV001062003, TOPMed rs2076734106, REVEL 0.39, ESM-1b 0.00, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- M6T (p.Met6Thr), rs781837406, ClinGen CA10458407, cosmic curated COSV11559, ClinVar RCV003143677, REVEL 0.28, ESM-1b 0.00, Uncertain significance, not provided
- M6V (p.Met6Val), rs782080475, ClinGen CA10458408, ClinVar RCV000801601, ClinVar RCV001566085, REVEL 0.33, ESM-1b 0.00, Conflicting interpretations, Alpha thalassemia-X-linked intellectual disability syndrome; not provided
- E8D (p.Glu8Asp), rs2148752831, ClinGen CA413724779, cosmic curated COSV64869, ClinVar RCV001563557, REVEL 0.36, ESM-1b 0.00, Uncertain significance, See cases; not provided; Alpha thalassemia-X-linked intellectual disability synd
- E8K (p.Glu8Lys), TOPMed rs2073484080, REVEL 0.47, ESM-1b 0.00
- S9N (p.Ser9Asn), rs1237969366, ClinGen CA413724772, ClinVar RCV003218888, TOPMed rs1237969366, ESM-1b 0.00, AlphaMissense 0.25, Uncertain significance, not provided
- S9R (p.Ser9Arg), Ensembl rs2148752769, REVEL 0.51, ESM-1b 0.00
- L11M (p.Leu11Met), Ensembl rs2148752727, ESM-1b 0.00, AlphaMissense 0.66
- N12K (p.Asn12Lys), ExAC rs782282345, gnomAD rs782282345, ESM-1b 0.00, AlphaMissense 0.72
- N12S (p.Asn12Ser), rs782399326, ClinGen CA10458393, ClinVar RCV001239681, ClinVar RCV002563952, REVEL 0.34, ESM-1b 0.00, Likely benign, not provided; Inborn genetic diseases; Alpha thalassemia-X-linked intellectual d
- T13S (p.Thr13Ser), Ensembl rs2148752663, ESM-1b 0.00, AlphaMissense 0.26
- H19R (p.His19Arg), rs2520310647, ClinGen CA413724703, ClinVar RCV002842201, ESM-1b 0.00, AlphaMissense 0.74, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- L22F (p.Leu22Phe), Ensembl rs2148752539, ESM-1b 0.00, AlphaMissense 0.88
- A23G (p.Ala23Gly), NCI-TCGA TCGA novel, ESM-1b 0.00, AlphaMissense 0.37, Variant assessed as somatic; moderate impact.
- A23P (p.Ala23Pro), TOPMed rs2073482326, ESM-1b 0.00, AlphaMissense 0.98
- H24N (p.His24Asn), cosmic curated COSV64869, TOPMed rs1191670776, gnomAD rs1191670776, REVEL 0.38, ESM-1b 0.00, Uncertain significance
- H24Y (p.His24Tyr), rs1191670776, ClinGen CA413724668, ClinVar RCV001042785, ClinVar RCV001759745, REVEL 0.47, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases; Alpha thalassemia-X-linked intellectual disability synd
- S26* (p.Ser26Ter), rs2073481839, ClinGen CA413724652, ClinVar RCV001255468, Ensembl rs2073481839, Likely pathogenic
- E27D (p.Glu27Asp), Ensembl rs1603268148, ESM-1b 0.00, AlphaMissense 0.19
- E30Q (p.Glu30Gln), rs1427263828, ClinGen CA413724627, ClinVar RCV000502021, TOPMed rs1427263828, REVEL 0.50, ESM-1b 0.00, Uncertain significance, not specified
- E31K (p.Glu31Lys), Ensembl rs2148752375, REVEL 0.34, ESM-1b 0.00
- S33N (p.Ser33Asn), rs2520309965, ClinGen CA413724603, ClinVar RCV002582332, ClinVar RCV005052005, ESM-1b 0.00, AlphaMissense 0.07, Uncertain significance, not provided; Alpha thalassemia-X-linked intellectual disability syndrome
- S34P (p.Ser34Pro), gnomAD rs1557165729, REVEL 0.59, ESM-1b 0.00
- P35L (p.Pro35Leu), Ensembl rs2148752322, ESM-1b 0.00, AlphaMissense 0.08
- P36S (p.Pro36Ser), TOPMed rs1463852072, gnomAD rs1463852072, REVEL 0.57, ESM-1b 0.00
- R37* (p.Arg37Ter), rs122445108, ClinGen CA121653, ClinVar RCV000012508, ClinVar RCV000148028, CADD 34.00, Pathogenic
- R37L (p.Arg37Leu), rs2148752220, ClinGen CA413724577, ClinVar RCV003512914, ESM-1b 0.00, AlphaMissense 0.08, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- R37Q (p.Arg37Gln), Ensembl rs2148752220, ESM-1b 0.00, AlphaMissense 0.08, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- A39S (p.Ala39Ser), Ensembl rs868945321, ESM-1b 0.00, AlphaMissense 0.07
- A39V (p.Ala39Val), rs2520309242, ClinGen CA413724565, ClinVar RCV003032696, REVEL 0.26, ESM-1b 0.00, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- M40V (p.Met40Val), rs149990714, ClinGen CA10458390, ClinVar RCV001279988, ESP rs149990714, ESM-1b 0.00, AlphaMissense 0.06, Benign, Alpha thalassemia-X-linked intellectual disability syndrome
- N43K (p.Asn43Lys), Ensembl rs2073478511, REVEL 0.22, ESM-1b 0.00
- N43T (p.Asn43Thr), ExAC rs782205682, gnomAD rs782205682, REVEL 0.25, ESM-1b 0.00
- T44K (p.Thr44Lys), gnomAD rs1557165675, REVEL 0.21, ESM-1b 0.00
- D45V (p.Asp45Val), rs1557151500, ClinGen CA413724495, ClinVar RCV000513135, ClinVar RCV003444562, REVEL 0.48, ESM-1b 0.00, Uncertain significance, not provided
- I47M (p.Ile47Met), Ensembl rs2148685938, ESM-1b 0.00, AlphaMissense 0.07
- I47T (p.Ile47Thr), rs2520173485, ClinGen CA413724478, ClinVar RCV003512790, ESM-1b 0.00, AlphaMissense 0.08, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- I47V (p.Ile47Val), rs782584831, ClinGen CA10458370, cosmic curated COSV10096, ClinVar RCV002255204, ESM-1b 0.00, AlphaMissense 0.06, Uncertain significance, not provided; Inborn genetic diseases
- S48C (p.Ser48Cys), rs1557151486, ClinGen CA413724476, ClinVar RCV001920051, gnomAD rs1557151486, REVEL 0.18, ESM-1b 0.00, Likely benign, Alpha thalassemia-X-linked intellectual disability syndrome
- S48G (p.Ser48Gly), rs1557151486, ClinGen CA413724475, ClinVar RCV003870631, gnomAD rs1557151486, REVEL 0.19, ESM-1b 0.00, Likely benign, Alpha thalassemia-X-linked intellectual disability syndrome
- S48I (p.Ser48Ile), TOPMed rs1326600949, ESM-1b 0.00, AlphaMissense 0.07
- G49T (p.Gly49Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S52G (p.Ser52Gly), TOPMed rs2072320800, REVEL 0.26, ESM-1b 0.00
- S54A (p.Ser54Ala), TOPMed rs2072320573, ESM-1b 0.00, AlphaMissense 0.07, Uncertain significance, not provided
- S54T (p.Ser54Thr), rs2072320573, ClinGen CA413724434, ClinVar RCV002000612, TOPMed rs2072320573, ESM-1b 0.00, AlphaMissense 0.06, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- D55G (p.Asp55Gly), rs1332942994, ClinGen CA413724424, ClinVar RCV003328781, TOPMed rs1332942994, REVEL 0.30, ESM-1b 0.00, Uncertain significance, not provided
- D55Y (p.Asp55Tyr), TOPMed rs2072320327, ESM-1b 0.31, AlphaMissense 0.15
- M56K (p.Met56Lys), rs782553856, ClinGen CA413724417, ClinVar RCV000697753, ExAC rs782553856, ESM-1b 0.00, AlphaMissense 0.09, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- M56T (p.Met56Thr), rs782553856, ClinGen CA10458369, ClinVar RCV002117482, ClinVar RCV006327441, ESM-1b 0.00, AlphaMissense 0.09, Conflicting interpretations, Alpha thalassemia-X-linked intellectual disability syndrome; Inborn genetic dise
- K61R (p.Lys61Arg), rs2072318858, ClinGen CA413724375, ClinVar RCV003624385, TOPMed rs2072318858, ESM-1b 0.00, AlphaMissense 0.07, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- G64* (p.Gly64Ter), Ensembl rs2148681763
- G64A (p.Gly64Ala), Ensembl rs2148681748, ESM-1b 0.00, AlphaMissense 0.09
- G64R (p.Gly64Arg), Ensembl rs2148681763, REVEL 0.65, ESM-1b 0.00
- T65I (p.Thr65Ile), Ensembl rs2148681705, ESM-1b 0.00, AlphaMissense 0.09, Uncertain significance
- T65N (p.Thr65Asn), rs2148681705, ClinGen CA413724335, ClinVar RCV003018585, REVEL 0.34, ESM-1b 0.00, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- T65S (p.Thr65Ser), Ensembl rs2148681705, ESM-1b 0.00, AlphaMissense 0.07, Uncertain significance
- S66N (p.Ser66Asn), Ensembl rs2148681656, REVEL 0.44, ESM-1b 0.00, Uncertain significance, not provided
- S66T (p.Ser66Thr), Ensembl rs2148681656, ESM-1b 0.00, AlphaMissense 0.07, Uncertain significance
- S67C (p.Ser67Cys), Ensembl rs2072256181, ESM-1b 0.00, AlphaMissense 0.09
- S68* (p.Ser68Ter), Ensembl rs2148681551
- S68I (p.Ser68Ile), Ensembl rs2072255674, ESM-1b 0.00, AlphaMissense 0.13
- S68L (p.Ser68Leu), cosmic curated COSV64870, Ensembl rs2148681551, REVEL 0.56, ESM-1b 0.00
- S68P (p.Ser68Pro), TOPMed rs2072255425, REVEL 0.64, ESM-1b 0.00
- E69Q (p.Glu69Gln), Ensembl rs2148681519, ESM-1b 0.00, AlphaMissense 0.15
- S71C (p.Ser71Cys), Ensembl rs2148681475, ESM-1b 0.34, AlphaMissense 0.08, Uncertain significance
- S71F (p.Ser71Phe), rs2148681475, ClinGen CA413724291, ClinVar RCV003624712, Ensembl rs2148681475, ESM-1b 0.29, AlphaMissense 0.08, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- S71Y (p.Ser71Tyr), Ensembl rs2148681475, ESM-1b 0.48, AlphaMissense 0.11, Uncertain significance
- K72M (p.Lys72Met), rs2148681433, ClinGen CA413724285, ClinVar RCV003860721, Ensembl rs2148681433, ESM-1b 0.00, AlphaMissense 0.27, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- K72N (p.Lys72Asn), Ensembl rs2148681410, ESM-1b 0.00, AlphaMissense 0.43, Likely benign
- S73C (p.Ser73Cys), Ensembl rs2148681365, ESM-1b 0.08, AlphaMissense 0.10
- S73T (p.Ser73Thr), Ensembl rs2148681386, ESM-1b 0.00, AlphaMissense 0.07
- S74* (p.Ser74Ter), Ensembl rs2148681341
- S74L (p.Ser74Leu), Ensembl rs2148681341, ESM-1b 0.00, AlphaMissense 0.06
- G75A (p.Gly75Ala), ExAC rs782198677, gnomAD rs782198677, ESM-1b 0.00, AlphaMissense 0.11, Uncertain significance
- G75E (p.Gly75Glu), cosmic curated COSV64869, ExAC rs782198677, gnomAD rs782198677, ESM-1b 0.00, AlphaMissense 0.41, Uncertain significance
- G75R (p.Gly75Arg), cosmic curated COSV64869, Ensembl rs2148681297, ESM-1b 0.00, AlphaMissense 0.44
- G75V (p.Gly75Val), rs782198677, ClinGen CA10458349, ClinVar RCV002004356, ExAC rs782198677, ESM-1b 0.00, AlphaMissense 0.12, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- G75T (p.Gly75Thr), NCI-TCGA Cosmic COSV6486, cosmic curated COSV64869, Variant assessed as somatic; high impact.
- S76L (p.Ser76Leu), rs782664370, ClinGen CA10458348, cosmic curated COSV10529, ClinVar RCV001514669, REVEL 0.34, ESM-1b 0.00, Benign, Alpha thalassemia-X-linked intellectual disability syndrome
- S76T (p.Ser76Thr), TOPMed rs1292971780, ESM-1b 0.00, AlphaMissense 0.08
- S76W (p.Ser76Trp), ExAC rs782664370, TOPMed rs782664370, gnomAD rs782664370, ESM-1b 1.00, AlphaMissense 0.32, Benign
- S77* (p.Ser77Ter), Ensembl rs2148681148
- S77T (p.Ser77Thr), Ensembl rs2148681173, ESM-1b 0.00, AlphaMissense 0.12
- R78* (p.Arg78Ter), cosmic curated COSV10606, NCI-TCGA TCGA novel, gnomAD rs2072254133, Variant assessed as somatic; high impact.
- R78G (p.Arg78Gly), gnomAD rs2072254133, ESM-1b 0.00, AlphaMissense 0.73
- R78L (p.Arg78Leu), rs2072253922, ClinGen CA413724250, ClinVar RCV003154415, ClinVar RCV004725666, ESM-1b 0.00, AlphaMissense 0.89, Conflicting interpretations, Alpha thalassemia-X-linked intellectual disability syndrome; Intellectual disabi
- R78P (p.Arg78Pro), TOPMed rs2072253922, ESM-1b 0.00, AlphaMissense 0.89, Likely benign
- R78Q (p.Arg78Gln), NCI-TCGA Cosmic COSV6487, cosmic curated COSV64870, TOPMed rs2072253922, REVEL 0.63, ESM-1b 0.00, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- S79* (p.Ser79Ter), rs122445107, ClinGen CA121651, cosmic curated COSV64870, ClinVar RCV000012507, Pathogenic
- S79P (p.Ser79Pro), Ensembl rs2148681058, ESM-1b 0.00, AlphaMissense 0.63
- S79T (p.Ser79Thr), Ensembl rs2148681058, ESM-1b 0.00, AlphaMissense 0.23
- K80* (p.Lys80Ter), cosmic curated COSV64869, Ensembl rs2148681016
- K80M (p.Lys80Met), Ensembl rs2148680999, ESM-1b 0.76, AlphaMissense 0.88
- K80N (p.Lys80Asn), Ensembl rs2148680968, ESM-1b 0.00, AlphaMissense 0.96
- R81G (p.Arg81Gly), Ensembl rs2148680946, ESM-1b 1.00, AlphaMissense 0.94
- R81K (p.Arg81Lys), Ensembl rs2148680931, ESM-1b 0.00, AlphaMissense 0.55
- S84A (p.Ser84Ala), rs1569540556, ClinGen CA413724198, ClinVar RCV001755523, Ensembl rs1569540556, REVEL 0.44, ESM-1b 0.00, Uncertain significance, not provided
- S84L (p.Ser84Leu), Ensembl rs2072206748, ESM-1b 0.00, AlphaMissense 0.18
- I85N (p.Ile85Asn), rs1402319857, ClinGen CA413724183, ClinVar RCV001963781, ClinVar RCV004970659, REVEL 0.39, ESM-1b 0.00, Conflicting interpretations, Inborn genetic diseases; Alpha thalassemia-X-linked intellectual disability synd
- I85T (p.Ile85Thr), cosmic curated COSV64869, TOPMed rs1402319857, gnomAD rs1402319857, REVEL 0.32, ESM-1b 0.00, Likely benign
- I85V (p.Ile85Val), rs150801485, ClinGen CA10458336, ClinVar RCV001051330, ClinVar RCV005408664, REVEL 0.34, ESM-1b 0.00, Conflicting interpretations, Alpha thalassemia-X-linked intellectual disability syndrome; not specified
- T87A (p.Thr87Ala), rs1557150036, ClinGen CA413724159, ClinVar RCV000519743, Ensembl rs1557150036, REVEL 0.59, ESM-1b 0.00, Uncertain significance, not provided
- T87I (p.Thr87Ile), Ensembl rs2072205781, REVEL 0.63, ESM-1b 0.00
- V90L (p.Val90Leu), ExAC rs781943078, TOPMed rs781943078, gnomAD rs781943078, ESM-1b 0.00, AlphaMissense 0.25, Uncertain significance, Inborn genetic diseases
- D93G (p.Asp93Gly), rs1064796774, ClinGen CA413724057, ClinVar RCV001817441, TOPMed rs1064796774, ESM-1b 0.99, AlphaMissense 0.10, Uncertain significance, not specified
- D93V (p.Asp93Val), rs1064796774, ClinGen CA16621509, ClinVar RCV000479685, ClinVar RCV001247873, REVEL 0.69, ESM-1b 1.00, Conflicting interpretations, Inborn genetic diseases; not provided; Alpha thalassemia-X-linked intellectual d
- D94N (p.Asp94Asn), TOPMed rs1311451690, ESM-1b 0.00, AlphaMissense 0.08
- D94Y (p.Asp94Tyr), TOPMed rs1311451690, ESM-1b 1.00, AlphaMissense 0.18
- E95* (p.Glu95Ter), Ensembl rs2072203556
- K96E (p.Lys96Glu), gnomAD rs1557149991, REVEL 0.35, ESM-1b 0.00
- L98F (p.Leu98Phe), 1000Genomes rs782388395, ExAC rs782388395, gnomAD rs782388395, REVEL 0.33, ESM-1b 0.00
- D99H (p.Asp99His), 1000Genomes rs782269589, ExAC rs782269589, gnomAD rs782269589, REVEL 0.46, ESM-1b 0.00
- D100G (p.Asp100Gly), rs782377443, ExAC rs782377443, gnomAD rs782377443, REVEL 0.39, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- E101A (p.Glu101Ala), TOPMed rs1557149948, gnomAD rs1557149948, NCI-TCGA Cosmic COSV1009, cosmic curated COSV10890, REVEL 0.54, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- V103A (p.Val103Ala), ExAC rs782208238, gnomAD rs782208238, ESM-1b 0.00, AlphaMissense 0.10
- V103I (p.Val103Ile), cosmic curated COSV10970, Ensembl rs2148677534, ESM-1b 0.00, AlphaMissense 0.07
- N104H (p.Asn104His), TOPMed rs2072200941, ESM-1b 0.00, AlphaMissense 0.08
- D106N (p.Asp106Asn), ExAC rs782614024, gnomAD rs782614024, REVEL 0.36, ESM-1b 0.00
- D106V (p.Asp106Val), TOPMed rs1285414081, gnomAD rs1285414081, REVEL 0.59, ESM-1b 0.00
- A107T (p.Ala107Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A107G (p.Ala107Gly), NCI-TCGA Cosmic COSV1009, ExAC rs782431661, TOPMed rs782431661, gnomAD rs782431661, REVEL 0.31, ESM-1b 0.00, Likely benign
- A107V (p.Ala107Val), rs782431661, ClinGen CA10458327, cosmic curated COSV10096, ClinVar RCV002646910, REVEL 0.32, ESM-1b 0.00, Likely benign, Alpha thalassemia-X-linked intellectual disability syndrome
- A107C (p.Ala107Cys), NCI-TCGA Cosmic COSV6486, cosmic curated COSV64869, Variant assessed as somatic; moderate impact.
- N109D (p.Asn109Asp), gnomAD rs1557149910, REVEL 0.33, ESM-1b 0.00
- E110D (p.Glu110Asp), gnomAD rs1557149904, REVEL 0.31, ESM-1b 0.00
- N111Y (p.Asn111Tyr), Ensembl rs2148677365, ESM-1b 0.00, AlphaMissense 0.17
- E113* (p.Glu113Ter), ExAC rs781803934, gnomAD rs781803934
- E113K (p.Glu113Lys), rs781803934, NCI-TCGA Cosmic COSV6486, cosmic curated COSV64869, ExAC rs781803934, REVEL 0.63, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- D115H (p.Asp115His), Ensembl rs2148677250, ESM-1b 0.00, AlphaMissense 0.41
- D115V (p.Asp115Val), rs1557149892, ClinGen CA413723793, ClinVar RCV002940573, ClinVar RCV003512190, REVEL 0.74, ESM-1b 0.00, Conflicting interpretations, Alpha thalassemia-X-linked intellectual disability syndrome; Inborn genetic dise
- I116V (p.Ile116Val), rs2072198606, ClinGen CA413723786, cosmic curated COSV10468, ClinVar RCV002576000, REVEL 0.37, ESM-1b 0.00, Uncertain significance, ATR-X-related syndrome; Alpha thalassemia-X-linked intellectual disability syndr
- Q119* (p.Gln119Ter), gnomAD rs1557149877, CADD 35.00
- Q119E (p.Gln119Glu), gnomAD rs1557149877, ESM-1b 0.00, AlphaMissense 0.09
- Q119H (p.Gln119His), rs959739617, ClinGen CA331569610, ClinVar RCV000547719, TOPMed rs959739617, REVEL 0.41, ESM-1b 0.00, Likely benign, Alpha thalassemia-X-linked intellectual disability syndrome
- K123E (p.Lys123Glu), gnomAD rs1355773607, REVEL 0.57, ESM-1b 1.00
- V126M (p.Val126Met), TOPMed rs2072041869, ESM-1b 1.00, AlphaMissense 0.63
- I127V (p.Ile127Val), gnomAD rs1569540319, REVEL 0.36, ESM-1b 0.00
- Q129* (p.Gln129Ter), Ensembl rs2148669922, CADD 35.00
- V133L (p.Val133Leu), rs2520122598, ClinGen CA413723050, ClinVar RCV003626021, ESM-1b 0.00, AlphaMissense 0.58, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- L134R (p.Leu134Arg), rs2520122502, ClinGen CA2695197158, ClinVar RCV003459814, ESM-1b 0.00, AlphaMissense 0.37, Pathogenic
- D137E (p.Asp137Glu), rs2520122405, ClinGen CA413723019, ClinVar RCV002815076, ESM-1b 0.00, AlphaMissense 0.14, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- D139Y (p.Asp139Tyr), rs2148669890, ClinGen CA413723007, ClinVar RCV002273678, Ensembl rs2148669890, ESM-1b 1.00, AlphaMissense 0.91, Uncertain significance, not provided
- P144H (p.Pro144His), Ensembl rs2148669828, ESM-1b 1.00, AlphaMissense 0.99
- P144T (p.Pro144Thr), ExAC rs782762156, gnomAD rs782762156, REVEL 0.72, ESM-1b 0.55
- S148N (p.Ser148Asn), Ensembl rs868948111, ESM-1b 0.00, AlphaMissense 0.42
- S150G (p.Ser150Gly), rs2072040574, ClinGen CA413722927, ClinVar RCV001045802, Ensembl rs2072040574, ESM-1b 0.00, AlphaMissense 0.28, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- S150T (p.Ser150Thr), Ensembl rs2148669783, ESM-1b 0.00, AlphaMissense 0.28
- T154G (p.Thr154Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- N156S (p.Asn156Ser), Ensembl rs2148669776, ESM-1b 0.00, AlphaMissense 0.09, Uncertain significance, not provided
- K158R (p.Lys158Arg), Ensembl rs892792649, ESM-1b 0.00, AlphaMissense 0.13
- K159R (p.Lys159Arg), TOPMed rs2072039854, ESM-1b 0.00, AlphaMissense 0.16
- R160C (p.Arg160Cys), TOPMed rs2072039368, REVEL 0.73, ESM-1b 0.00
- R160H (p.Arg160His), rs2072039122, ClinGen CA413722848, NCI-TCGA Cosmic COSV1009, ClinVar RCV001329932, REVEL 0.59, ESM-1b 0.00, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome; Acquired hemoglobin
- G161E (p.Gly161Glu), Ensembl rs2072038407, REVEL 0.55, ESM-1b 0.00
- G161R (p.Gly161Arg), rs1569540314, ClinGen CA413722846, ClinVar RCV002149311, Ensembl rs1569540314, REVEL 0.44, ESM-1b 0.00, Likely benign, Alpha thalassemia-X-linked intellectual disability syndrome
- E162* (p.Glu162Ter), Ensembl rs2148669662
- D163E (p.Asp163Glu), rs2520079088, ClinGen CA413722811, ClinVar RCV003625506, ESM-1b 0.00, AlphaMissense 0.31, Uncertain significance, Alpha thalassemia-X-linked intellectual disability syndrome
- D163G (p.Asp163Gly), Ensembl rs2071731492, REVEL 0.63, ESM-1b 1.00
- D163V (p.Asp163Val), Ensembl rs2071731492, ESM-1b 1.00, AlphaMissense 0.81
- G164A (p.Gly164Ala), 1000Genomes rs782707997, ExAC rs782707997, gnomAD rs782707997, ESM-1b 0.39, AlphaMissense 0.52
- G164V (p.Gly164Val), 1000Genomes rs782707997, ExAC rs782707997, gnomAD rs782707997, REVEL 0.53, ESM-1b 1.00
- L165F (p.Leu165Phe), TOPMed rs2071730774, ESM-1b 1.00, AlphaMissense 0.86
- H166D (p.His166Asp), Ensembl rs2148657371, ESM-1b 1.00, AlphaMissense 0.96
- H166L (p.His166Leu), Ensembl rs2148657354, ESM-1b 1.00, AlphaMissense 0.75, Uncertain significance
- H166R (p.His166Arg), rs2148657354, ClinGen CA413722786, ClinVar RCV002878097, Ensembl rs2148657354, ESM-1b 1.00, AlphaMissense 0.83, Uncertain significance, Inborn genetic diseases
- H166Y (p.His166Tyr), cosmic curated COSV10529, Ensembl rs2148657371, ESM-1b 1.00, AlphaMissense 0.70
- G167A (p.Gly167Ala), Ensembl rs2148657294, ESM-1b 1.00, AlphaMissense 0.94
- G167E (p.Gly167Glu), Ensembl rs2148657294, ESM-1b 1.00, AlphaMissense 1.00
- G167R (p.Gly167Arg), Ensembl rs2148657321, ESM-1b 1.00, AlphaMissense 1.00
- G167V (p.Gly167Val), cosmic curated COSV64870, Ensembl rs2148657294, ESM-1b 1.00, AlphaMissense 0.99
- I168S (p.Ile168Ser), cosmic curated COSV64869, Ensembl rs2148657268, ESM-1b 1.00, AlphaMissense 1.00
- V169E (p.Val169Glu), Ensembl rs2148657234, ESM-1b 1.00, AlphaMissense 1.00
- V169L (p.Val169Leu), Ensembl rs2148657246, ESM-1b 0.81, AlphaMissense 0.97
Public ATRX analysis runs
- ATRX analysis run — ATRX (7,549 variants) — completed 2026-10-09