SATB2 (DNA-binding protein SATB2) variants and mutations
SATB2 (also known as DNA-binding protein SATB2) is a human protein-coding gene encoding a DNA-binding protein. A DNA-binding chromatin organizer that regulates developmental gene expression. Variants can cause a syndrome affecting speech, cognition, teeth, and palate development. This analysis covers 1,153 SATB2 variants and mutations. Of these, 94% have computational variant effect predictions. Disease context includes chromosome 2q32-q33 deletion syndrome, cleft palate, and Intellectual disability. Example SATB2 variants include M1V, R3L, and R3P.
Variant analysis overview
- Gene: SATB2
- Protein: DNA-binding protein SATB2
- UniProt accession: Q9UPW6
- Organism: Homo sapiens
- Variants analyzed: 1153
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 944 unspecified-consequence records; 1 stop retained variant; 1 stop-gained variants; 89 missense variants; 163 synonymous variants; 3 frameshift variants; 3 in-frame deletions; 4 splice-region variants; 4 substitution
- Prediction scores: 1,087 variants have prediction scores (94% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: chromosome 2q32-q33 deletion syndrome, cleft palate, Intellectual disability, isolated cleft palate, SATB2 associated disorder, hereditary disease, Abnormality of the skeletal system, mathematical ability, schizophrenia, ulcerative colitis, colorectal cancer, inflammatory bowel disease.
Protein structure and variant hotspots
- Protein features: 2 domains; 5 post-translational modification sites.
- Structural context: 166 variants have structural context.
- PTM context: 10 variants overlap post-translational modification sites.
- Experimental data: 152 protein positions have experimental scores. Source: SATB2 CUT domain domainome 1.0.
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 SATB2
Notable SATB2 variants
Examples include M1V, R3L, R3P, R4Q, R4W, S5N, S5R, E6K. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1V (p.Met1Val), rs1553507391, ClinGen CA350388705, ClinVar RCV000578907, ESM-1b 1.00, AlphaMissense 0.18, Likely pathogenic, not provided
- R3L (p.Arg3Leu), cosmic curated COSV53491, REVEL 0.24, ESM-1b 0.00
- R3P (p.Arg3Pro), rs2469070040, ClinGen CA350388686, ClinVar RCV003742019, REVEL 0.24, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- R4Q (p.Arg4Gln), gnomAD rs1463296675, REVEL 0.24, ESM-1b 0.00
- R4W (p.Arg4Trp), cosmic curated COSV53489, REVEL 0.24, ESM-1b 1.00
- S5N (p.Ser5Asn), rs2469070022, ClinGen CA350388676, ClinVar RCV003582002, REVEL 0.14, ESM-1b 0.63, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- S5R (p.Ser5Arg), rs2469070015, ClinGen CA350388672, ClinVar RCV003741747, cosmic curated COSV53487, REVEL 0.29, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- E6K (p.Glu6Lys), gnomAD rs1434320727, REVEL 0.29, ESM-1b 0.17
- P8Q (p.Pro8Gln), rs2105957352, ClinGen CA350388653, ClinVar RCV001774069, ClinVar RCV005094982, REVEL 0.38, ESM-1b 0.67, Uncertain significance, Chromosome 2q32-q33 deletion syndrome; not provided
- P8S (p.Pro8Ser), Ensembl rs568095706, REVEL 0.37, ESM-1b 0.00
- C9R (p.Cys9Arg), TOPMed rs1361158169, REVEL 0.12, ESM-1b 0.00
- C9S (p.Cys9Ser), gnomAD rs1209144312, ESM-1b 0.00, AlphaMissense 0.10
- R11P (p.Arg11Pro), TOPMed rs1692262207, gnomAD rs1692262207, ESM-1b 0.00, AlphaMissense 0.25
- R11Q (p.Arg11Gln), TOPMed rs1692262207, gnomAD rs1692262207, REVEL 0.12, ESM-1b 0.00
- D12N (p.Asp12Asn), gnomAD rs1282358129, REVEL 0.11, ESM-1b 0.00
- R16P (p.Arg16Pro), rs1295030903, ClinGen CA350388600, ClinVar RCV003832916, REVEL 0.25, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- R16Q (p.Arg16Gln), gnomAD rs1295030903, REVEL 0.16, ESM-1b 0.00, Uncertain significance
- S18R (p.Ser18Arg), ExAC rs747894251, gnomAD rs747894251, REVEL 0.18, ESM-1b 0.00
- G19C (p.Gly19Cys), cosmic curated COSV53493, REVEL 0.27, ESM-1b 0.00
- S20I (p.Ser20Ile), Ensembl rs1692261395, REVEL 0.24, ESM-1b 1.00
- S20N (p.Ser20Asn), Ensembl rs1692261395, REVEL 0.11, ESM-1b 1.00
- P21R (p.Pro21Arg), cosmic curated COSV53478, ESM-1b 0.57, AlphaMissense 0.18
- D22E (p.Asp22Glu), TOPMed rs1405630119, gnomAD rs1405630119, REVEL 0.06, ESM-1b 0.00
- V23F (p.Val23Phe), rs2469069862, ClinGen CA350388555, ClinVar RCV002734885, ClinVar RCV003232658, REVEL 0.14, ESM-1b 0.00, Uncertain significance, not provided; Chromosome 2q32-q33 deletion syndrome
- V23L (p.Val23Leu), rs2469069862, ClinGen CA350388556, ClinVar RCV003032306, ESM-1b 0.00, AlphaMissense 0.08, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- K24R (p.Lys24Arg), rs1176416627, ClinGen CA350388547, ClinVar RCV002046749, TOPMed rs1176416627, REVEL 0.05, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- G25A (p.Gly25Ala), rs2469069847, ClinGen CA350388539, ClinVar RCV002889550, ESM-1b 0.00, AlphaMissense 0.09, Benign, Chromosome 2q32-q33 deletion syndrome
- P26A (p.Pro26Ala), rs1473042227, ClinGen CA350388536, ClinVar RCV001373401, TOPMed rs1473042227, REVEL 0.18, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- P26S (p.Pro26Ser), cosmic curated COSV53481, REVEL 0.19, ESM-1b 0.00
- P27L (p.Pro27Leu), cosmic curated COSV53489, ESM-1b 1.00, AlphaMissense 0.09
- P27S (p.Pro27Ser), TOPMed rs989025045, gnomAD rs989025045, REVEL 0.34, ESM-1b 1.00
- P28A (p.Pro28Ala), Ensembl rs1559066045, REVEL 0.21, ESM-1b 0.00
- P28S (p.Pro28Ser), cosmic curated COSV53480, REVEL 0.17, ESM-1b 0.24
- K30* (p.Lys30Ter), Ensembl rs1574645369, Uncertain significance
- K30E (p.Lys30Glu), rs1574645369, ClinGen CA350388512, ClinVar RCV001198892, Ensembl rs1574645369, ESM-1b 1.00, AlphaMissense 0.48, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- K30N (p.Lys30Asn), gnomAD rs1176548430, REVEL 0.20, ESM-1b 1.00
- V31M (p.Val31Met), rs2469069776, ClinGen CA350388506, ClinVar RCV003741898, ESM-1b 0.00, AlphaMissense 0.09, Benign, Chromosome 2q32-q33 deletion syndrome
- A32T (p.Ala32Thr), rs1461281024, ClinGen CA350388499, ClinVar RCV001297369, gnomAD rs1461281024, REVEL 0.19, ESM-1b 0.30, Benign, Chromosome 2q32-q33 deletion syndrome
- R33W (p.Arg33Trp), rs1392839872, ClinGen CA350388493, ClinVar RCV004450255, gnomAD rs1392839872, REVEL 0.64, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases
- L34Q (p.Leu34Gln), rs2469069751, ClinGen CA350388487, ClinVar RCV003443296, ESM-1b 1.00, AlphaMissense 0.25, Uncertain significance, not provided
- E35G (p.Glu35Gly), cosmic curated COSV10502, REVEL 0.35, ESM-1b 1.00
- Q36H (p.Gln36His), rs1165492597, ClinGen CA350388470, ClinVar RCV003115526, gnomAD rs1165492597, REVEL 0.12, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- G38C (p.Gly38Cys), rs1458922428, ClinGen CA350388458, ClinVar RCV002045755, gnomAD rs1458922428, REVEL 0.50, ESM-1b 0.88, Likely benign, Chromosome 2q32-q33 deletion syndrome
- G38S (p.Gly38Ser), gnomAD rs1458922428, REVEL 0.39, ESM-1b 0.00, Likely benign
- S39G (p.Ser39Gly), cosmic curated COSV10879, REVEL 0.21, ESM-1b 0.00
- S39N (p.Ser39Asn), gnomAD rs1208341343, ESM-1b 0.13, AlphaMissense 0.61
- P40A (p.Pro40Ala), rs1191904885, ClinGen CA350388445, ClinVar RCV001034093, gnomAD rs1191904885, REVEL 0.41, ESM-1b 0.00, Likely benign, Chromosome 2q32-q33 deletion syndrome
- P40S (p.Pro40Ser), gnomAD rs1191904885, REVEL 0.40, ESM-1b 0.00, Benign
- P40T (p.Pro40Thr), rs1191904885, ClinGen CA350388446, ClinVar RCV003741991, REVEL 0.42, ESM-1b 0.00, Conflicting interpretations, Chromosome 2q32-q33 deletion syndrome; not provided
- M41V (p.Met41Val), rs919635073, ClinGen CA64293422, ClinVar RCV002087556, gnomAD rs919635073, REVEL 0.09, ESM-1b 0.00, Benign, Chromosome 2q32-q33 deletion syndrome
- G42* (p.Gly42Ter), rs1064793947, ClinGen CA16617415, ClinVar RCV000486598, Ensembl rs1064793947, CADD 37.00, Pathogenic
- A43T (p.Ala43Thr), TOPMed rs1249539770, gnomAD rs1249539770, REVEL 0.05, ESM-1b 0.00, Conflicting interpretations, Chromosome 2q32-q33 deletion syndrome; Inborn genetic diseases
- R44C (p.Arg44Cys), cosmic curated COSV53478, REVEL 0.48, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome; not provided
- R46W (p.Arg46Trp), cosmic curated COSV53478, ESM-1b 0.00, AlphaMissense 0.23, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- P47L (p.Pro47Leu), rs1692259118, ClinGen CA350388397, ClinVar RCV001205401, Ensembl rs1692259118, REVEL 0.12, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- N48D (p.Asn48Asp), gnomAD rs1188890432, REVEL 0.22, ESM-1b 0.00
- N48S (p.Asn48Ser), gnomAD rs1467878282, REVEL 0.11, ESM-1b 0.00, Uncertain significance
- N48T (p.Asn48Thr), rs1467878282, ClinGen CA350388393, ClinVar RCV003741795, ESM-1b 0.00, AlphaMissense 0.06, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- A50S (p.Ala50Ser), rs2469069641, ClinGen CA350388380, ClinVar RCV003024500, REVEL 0.07, ESM-1b 0.00, Benign, Chromosome 2q32-q33 deletion syndrome
- V51G (p.Val51Gly), Ensembl rs2105957121, ESM-1b 0.00, AlphaMissense 0.07
- V51M (p.Val51Met), rs540871216, ClinGen CA2046160, ClinVar RCV001510105, ClinVar RCV002568013, REVEL 0.08, ESM-1b 0.00, Benign/Likely benign, Inborn genetic diseases; Chromosome 2q32-q33 deletion syndrome
- A52V (p.Ala52Val), rs1357016064, ClinGen CA350388366, ClinVar RCV000762309, TOPMed rs1357016064, REVEL 0.06, ESM-1b 0.00, Uncertain significance, not provided
- K53E (p.Lys53Glu), rs2469069600, ClinGen CA350388365, ClinVar RCV003304366, REVEL 0.11, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases
- K53R (p.Lys53Arg), rs2469069594, ClinGen CA350388361, ClinVar RCV003142743, REVEL 0.07, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- A54S (p.Ala54Ser), TOPMed rs1446614613, gnomAD rs1446614613, REVEL 0.10, ESM-1b 0.00
- V55A (p.Val55Ala), rs1226310700, ClinGen CA350388349, ClinVar RCV003740997, TOPMed rs1226310700, REVEL 0.13, ESM-1b 0.00, Benign, Chromosome 2q32-q33 deletion syndrome
- V55L (p.Val55Leu), rs748892556, ClinGen CA2046159, ClinVar RCV001242202, ClinVar RCV001560958, REVEL 0.07, ESM-1b 0.00, Likely benign, Chromosome 2q32-q33 deletion syndrome; not provided; Inborn genetic diseases
- V55M (p.Val55Met), rs748892556, ClinGen CA350388351, ClinVar RCV002762702, ClinVar RCV005099622, REVEL 0.08, ESM-1b 0.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome; Inborn genetic diseases
- M59V (p.Met59Val), gnomAD rs1478238325, REVEL 0.30, ESM-1b 1.00
- I60L (p.Ile60Leu), Ensembl rs2105929068, REVEL 0.11, ESM-1b 0.00
- P61S (p.Pro61Ser), NCI-TCGA Cosmic COSV9961, cosmic curated COSV99612, ESM-1b 1.00, AlphaMissense 1.00, Variant assessed as somatic; moderate impact.
- V62D (p.Val62Asp), rs1064796649, ClinGen CA16617414, ClinVar RCV000479021, Ensembl rs1064796649, ESM-1b 1.00, AlphaMissense 1.00, Likely pathogenic, not provided
- C64A (p.Cys64Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- C64T (p.Cys64Thr), rs1367686940, gnomAD rs1367686940, AlphaMissense 0.13, MetaLR 0.40, Variant assessed as somatic; moderate impact.
- V65F (p.Val65Phe), cosmic curated COSV10502, NCI-TCGA TCGA novel, ESM-1b 1.00, AlphaMissense 0.88, Variant assessed as somatic; moderate impact.
- V65I (p.Val65Ile), ExAC rs749125541, gnomAD rs749125541, REVEL 0.08, ESM-1b 1.00
- V66M (p.Val66Met), cosmic curated COSV53488, TOPMed rs1252596825, gnomAD rs1252596825, REVEL 0.22, ESM-1b 0.86
- Q68E (p.Gln68Glu), rs2469034270, ClinGen CA350386923, ClinVar RCV003066199, REVEL 0.26, ESM-1b 1.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- L69M (p.Leu69Met), ExAC rs745323861, TOPMed rs745323861, gnomAD rs745323861, REVEL 0.07, ESM-1b 0.00, Likely benign
- D70Y (p.Asp70Tyr), cosmic curated COSV10961, ESM-1b 1.00, AlphaMissense 0.50
- G71C (p.Gly71Cys), ExAC rs756865617, TOPMed rs756865617, gnomAD rs756865617, REVEL 0.04, ESM-1b 1.00, Benign
- G71S (p.Gly71Ser), rs756865617, ClinGen CA2046136, cosmic curated COSV99613, ClinVar RCV000818908, REVEL 0.07, ESM-1b 1.00, Benign, Chromosome 2q32-q33 deletion syndrome
- G71V (p.Gly71Val), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53482, ESM-1b 1.00, AlphaMissense 0.09, Variant assessed as somatic; moderate impact.
- S72C (p.Ser72Cys), rs755238845, ClinGen CA2046134, ClinVar RCV003742187, ClinVar RCV004661726, REVEL 0.14, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases; Chromosome 2q32-q33 deletion syndrome
- S72F (p.Ser72Phe), NCI-TCGA Cosmic COSV5347, cosmic curated COSV53477, ESM-1b 1.00, AlphaMissense 0.13, Variant assessed as somatic; moderate impact.
- S72P (p.Ser72Pro), rs753249521, ClinGen CA2046135, ClinVar RCV003054715, ClinVar RCV004960918, REVEL 0.04, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases; Chromosome 2q32-q33 deletion syndrome
- S72T (p.Ser72Thr), ExAC rs753249521, TOPMed rs753249521, gnomAD rs753249521, REVEL 0.08, ESM-1b 0.00, Uncertain significance
- S72Y (p.Ser72Tyr), ExAC rs755238845, gnomAD rs755238845, REVEL 0.10, ESM-1b 1.00, Uncertain significance
- Y75* (p.Tyr75Ter), rs1357010510, ClinGen CA350386876, ClinVar RCV000995632, gnomAD rs1357010510, Pathogenic
- Y75C (p.Tyr75Cys), ExAC rs750686286, TOPMed rs750686286, gnomAD rs750686286, REVEL 0.12, ESM-1b 1.00
- Y75H (p.Tyr75His), rs760905348, ClinGen CA2046130, ClinVar RCV001408476, ExAC rs760905348, REVEL 0.06, ESM-1b 1.00, Likely benign, Chromosome 2q32-q33 deletion syndrome
- R78K (p.Arg78Lys), rs767582582, ClinGen CA2046128, cosmic curated COSV10459, ClinVar RCV001368812, REVEL 0.09, ESM-1b 0.00, Benign, Chromosome 2q32-q33 deletion syndrome
- R78T (p.Arg78Thr), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53482, ESM-1b 0.50, AlphaMissense 0.44, Variant assessed as somatic; moderate impact.
- E79G (p.Glu79Gly), rs2469034184, ClinGen CA350386849, ClinVar RCV003322986, ESM-1b 1.00, AlphaMissense 0.58, Uncertain significance, not provided
- A82S (p.Ala82Ser), rs979695165, ClinGen CA64291164, ClinVar RCV002734567, ClinVar RCV003741328, REVEL 0.26, ESM-1b 1.00, Uncertain significance, SATB2-related disorder; Chromosome 2q32-q33 deletion syndrome; Inborn genetic di
- A82T (p.Ala82Thr), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53483, TOPMed rs979695165, REVEL 0.25, ESM-1b 1.00, Uncertain significance
- E83D (p.Glu83Asp), cosmic curated COSV53487, ESM-1b 1.00, AlphaMissense 0.79
- E83K (p.Glu83Lys), NCI-TCGA Cosmic COSV5349, cosmic curated COSV53490, gnomAD rs1691562317, REVEL 0.27, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- F84V (p.Phe84Val), 1000Genomes rs548822205, ESM-1b 1.00, AlphaMissense 1.00
- V87L (p.Val87Leu), cosmic curated COSV53482, ESM-1b 1.00, AlphaMissense 0.63
- R88G (p.Arg88Gly), NCI-TCGA Cosmic COSV5348, NCI-TCGA Cosmic COSV9961, cosmic curated COSV99612, REVEL 0.40, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- R88Q (p.Arg88Gln), rs530118484, ClinGen CA2046124, NCI-TCGA Cosmic COSV5348, cosmic curated COSV53484, REVEL 0.35, ESM-1b 1.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- R88W (p.Arg88Trp), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53484, NCI-TCGA Cosmic COSV9961, REVEL 0.41, ESM-1b 1.00, Likely pathogenic, Chromosome 2q32-q33 deletion syndrome
- K89R (p.Lys89Arg), rs769528257, ClinGen CA2046122, ClinVar RCV002621002, ClinVar RCV002621003, REVEL 0.04, ESM-1b 0.00, Conflicting interpretations, Inborn genetic diseases; Chromosome 2q32-q33 deletion syndrome
- L92P (p.Leu92Pro), rs746334982, ClinGen CA64291161, ClinVar RCV003026672, TOPMed rs746334982, REVEL 0.58, ESM-1b 0.68, Benign, Chromosome 2q32-q33 deletion syndrome
- L96R (p.Leu96Arg), rs1064795247, ClinGen CA16617413, ClinVar RCV000485845, Ensembl rs1064795247, ESM-1b 1.00, AlphaMissense 1.00, Likely pathogenic, not provided
- E98D (p.Glu98Asp), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53486, REVEL 0.15, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- A100V (p.Ala100Val), TOPMed rs1691560643, REVEL 0.39, ESM-1b 1.00
- L101P (p.Leu101Pro), rs2469034035, ClinGen CA350386704, ClinVar RCV004450254, ESM-1b 1.00, AlphaMissense 1.00, Likely pathogenic, Inborn genetic diseases
- L102P (p.Leu102Pro), gnomAD rs1691560087, REVEL 0.60, ESM-1b 1.00
- L104M (p.Leu104Met), cosmic curated COSV53481, ESM-1b 1.00, AlphaMissense 0.89
- L104V (p.Leu104Val), TOPMed rs1180201896, ESM-1b 1.00, AlphaMissense 0.96
- Y106* (p.Tyr106Ter), rs1330378388, ClinGen CA350386673, ClinVar RCV001249707, gnomAD rs1330378388, Pathogenic
- Y106H (p.Tyr106His), cosmic curated COSV53479, ESM-1b 1.00, AlphaMissense 1.00
- S107F (p.Ser107Phe), cosmic curated COSV99612, ESM-1b 1.00, AlphaMissense 0.99
- S107Y (p.Ser107Tyr), cosmic curated COSV53485, ESM-1b 1.00, AlphaMissense 0.99
- H108D (p.His108Asp), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53483, ESM-1b 1.00, AlphaMissense 0.97, Variant assessed as somatic; moderate impact.
- H108Q (p.His108Gln), NCI-TCGA Cosmic COSV9961, cosmic curated COSV99610, ESM-1b 1.00, AlphaMissense 0.91, Variant assessed as somatic; moderate impact.
- S109T (p.Ser109Thr), cosmic curated COSV53487, ESM-1b 0.00, AlphaMissense 0.18
- A111E (p.Ala111Glu), cosmic curated COSV53488, ESM-1b 1.00, AlphaMissense 1.00
- A111V (p.Ala111Val), rs1376331026, ClinGen CA350386639, NCI-TCGA Cosmic COSV5348, cosmic curated COSV53483, REVEL 0.45, ESM-1b 1.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome; not provided
- A112T (p.Ala112Thr), rs2105928809, ClinGen CA350386638, ClinVar RCV002260561, Ensembl rs2105928809, ESM-1b 1.00, AlphaMissense 0.67, Uncertain significance, SATB2 associated disorder
- A112V (p.Ala112Val), NCI-TCGA Cosmic COSV9961, cosmic curated COSV99611, ESM-1b 1.00, AlphaMissense 0.64, Variant assessed as somatic; moderate impact.
- Q113* (p.Gln113Ter), rs1559052053, ClinGen CA350386630, ClinVar RCV000760901, Ensembl rs1559052053, Pathogenic
- Q113H (p.Gln113His), gnomAD rs1691558786, REVEL 0.24, ESM-1b 1.00
- Q115* (p.Gln115Ter), rs1559052032, ClinGen CA350386616, ClinVar RCV000695069, ClinVar RCV003258931, AlphaMissense 0.19, MetaLR 0.09, Pathogenic
- Q115E (p.Gln115Glu), rs1559052032, ClinGen CA350386617, ClinVar RCV001367278, Ensembl rs1559052032, ESM-1b 1.00, AlphaMissense 0.19, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- Q115H (p.Gln115His), cosmic curated COSV11348, ESM-1b 0.43, AlphaMissense 0.22
- G116E (p.Gly116Glu), cosmic curated COSV10502, ESM-1b 1.00, AlphaMissense 1.00
- G116R (p.Gly116Arg), rs1131691672, ClinGen CA350386609, ClinVar RCV000494383, Ensembl rs1131691672, ESM-1b 1.00, AlphaMissense 1.00, Pathogenic/Likely pathogenic, Chromosome 2q32-q33 deletion syndrome; not provided
- I118T (p.Ile118Thr), rs2468949079, ClinGen CA350389291, ClinVar RCV003990888, ESM-1b 1.00, AlphaMissense 1.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- K119N (p.Lys119Asn), TOPMed rs1185687010, ESM-1b 1.00, AlphaMissense 0.97, Likely benign
- G121* (p.Gly121Ter), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53483, Variant assessed as somatic; high impact.
- G121C (p.Gly121Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- R122K (p.Arg122Lys), rs1182083147, ClinGen CA350389268, ClinVar RCV003741388, NCI-TCGA TCGA novel, ESM-1b 0.00, AlphaMissense 0.53, Benign, Chromosome 2q32-q33 deletion syndrome
- R122M (p.Arg122Met), gnomAD rs1182083147, ESM-1b 1.00, AlphaMissense 0.68, Benign
- R122S (p.Arg122Ser), TOPMed rs1689786468, REVEL 0.36, ESM-1b 1.00, Uncertain significance, not provided
- R122T (p.Arg122Thr), rs1182083147, ClinGen CA350389267, ClinVar RCV001887054, gnomAD rs1182083147, ESM-1b 1.00, AlphaMissense 0.53, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- W123* (p.Trp123Ter), rs2468949035, ClinGen CA350389260, ClinVar RCV004545486, ClinVar RCV005003744, Pathogenic
- N124T (p.Asn124Thr), Ensembl rs1574568732, ESM-1b 1.00, AlphaMissense 0.32
- P125S (p.Pro125Ser), rs2468949021, ClinGen CA350389244, ClinVar RCV002462622, ESM-1b 0.76, AlphaMissense 0.94, Uncertain significance, not provided
- L126F (p.Leu126Phe), rs1574568704, ClinGen CA350389239, ClinVar RCV001027981, Ensembl rs1574568704, REVEL 0.41, ESM-1b 1.00, Benign, Chromosome 2q32-q33 deletion syndrome
- P127S (p.Pro127Ser), cosmic curated COSV10729, ESM-1b 0.54, AlphaMissense 0.78
- L128F (p.Leu128Phe), Ensembl rs2105867984, REVEL 0.35, ESM-1b 1.00
- S129I (p.Ser129Ile), cosmic curated COSV99613, ESM-1b 1.00, AlphaMissense 0.34
- Y130C (p.Tyr130Cys), rs372822699, ClinGen CA2046097, ClinVar RCV000997640, ClinVar RCV003741243, REVEL 0.35, ESM-1b 1.00, Conflicting interpretations, not provided; Inborn genetic diseases; Chromosome 2q32-q33 deletion syndrome
- Y130H (p.Tyr130His), NCI-TCGA Cosmic COSV9961, cosmic curated COSV99612, ESM-1b 0.47, AlphaMissense 0.24, Variant assessed as somatic; moderate impact.
- V131E (p.Val131Glu), rs1064794638, ClinGen CA16617412, ClinVar RCV000485195, Ensembl rs1064794638, ESM-1b 1.00, AlphaMissense 0.99, Likely pathogenic, not provided
- V131L (p.Val131Leu), rs1689785051, ClinGen CA350389206, ClinVar RCV001327321, gnomAD rs1689785051, REVEL 0.24, ESM-1b 1.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome; not provided
- T132K (p.Thr132Lys), cosmic curated COSV53490, ESM-1b 1.00, AlphaMissense 0.99
- T132P (p.Thr132Pro), cosmic curated COSV53484, ESM-1b 1.00, AlphaMissense 0.97
- D133E (p.Asp133Glu), rs1574568652, ClinGen CA350389190, ClinVar RCV003581750, Ensembl rs1574568652, REVEL 0.41, ESM-1b 0.00, Likely benign, Chromosome 2q32-q33 deletion syndrome
- D133Y (p.Asp133Tyr), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53489, ESM-1b 1.00, AlphaMissense 0.88, Variant assessed as somatic; moderate impact.
- A134V (p.Ala134Val), TOPMed rs1689784754, gnomAD rs1689784754, REVEL 0.25, ESM-1b 1.00
- D136G (p.Asp136Gly), NCI-TCGA Cosmic COSV5347, cosmic curated COSV53477, ESM-1b 1.00, AlphaMissense 0.50, Variant assessed as somatic; moderate impact.
- D136N (p.Asp136Asn), cosmic curated COSV53477, ESM-1b 1.00, AlphaMissense 0.32
- A137T (p.Ala137Thr), cosmic curated COSV53480, TOPMed rs1454219036, gnomAD rs1454219036, REVEL 0.33, ESM-1b 1.00, Uncertain significance, not specified
- A137V (p.Ala137Val), rs746240750, ClinGen CA2046092, ClinVar RCV001368566, ClinVar RCV003883618, REVEL 0.16, ESM-1b 1.00, Uncertain significance, not provided; Chromosome 2q32-q33 deletion syndrome
- V139A (p.Val139Ala), rs1689783884, ClinGen CA350389153, ClinVar RCV001311976, Ensembl rs1689783884, ESM-1b 1.00, AlphaMissense 0.98, Uncertain significance, not provided
- A140P (p.Ala140Pro), cosmic curated COSV10436, ESM-1b 1.00, AlphaMissense 0.99
- D141E (p.Asp141Glu), gnomAD rs1401692784, REVEL 0.51, ESM-1b 1.00
- D141N (p.Asp141Asn), NCI-TCGA Cosmic COSV9961, cosmic curated COSV99610, ESM-1b 1.00, AlphaMissense 0.68, Variant assessed as somatic; moderate impact.
- M142I (p.Met142Ile), rs764205432, ClinGen CA2046088, ClinVar RCV001221058, ClinVar RCV003438723, REVEL 0.47, ESM-1b 1.00, Conflicting interpretations, Inborn genetic diseases; Chromosome 2q32-q33 deletion syndrome; not provided
- M142V (p.Met142Val), rs751779659, ClinGen CA2046089, ClinVar RCV001892193, ExAC rs751779659, REVEL 0.45, ESM-1b 1.00, Conflicting interpretations, Chromosome 2q32-q33 deletion syndrome
- Q144* (p.Gln144Ter), rs1689783166, ClinGen CA350389123, ClinVar RCV003317025, AlphaMissense 0.19, MetaLR 0.49, Pathogenic
- Q144E (p.Gln144Glu), TOPMed rs1689783166, gnomAD rs1689783166, REVEL 0.26, ESM-1b 1.00, Pathogenic
- Q144K (p.Gln144Lys), cosmic curated COSV53485, ESM-1b 1.00, AlphaMissense 0.28
- D145E (p.Asp145Glu), TOPMed rs1559017829, REVEL 0.43, ESM-1b 1.00, Likely benign
- D145N (p.Asp145Asn), TOPMed rs1689782944, ESM-1b 1.00, AlphaMissense 0.83
- V149A (p.Val149Ala), rs765278258, ClinGen CA2046085, ClinVar RCV001763873, ClinVar RCV006467893, REVEL 0.44, ESM-1b 1.00, Uncertain significance, Chromosome 2q32-q33 deletion syndrome; not provided
- V150A (p.Val150Ala), NCI-TCGA Cosmic COSV9961, cosmic curated COSV99610, REVEL 0.45, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- T151M (p.Thr151Met), rs1414878673, ClinGen CA350389071, cosmic curated COSV99613, ClinVar RCV002755823, REVEL 0.48, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases; Chromosome 2q32-q33 deletion syndrome
- Q157R (p.Gln157Arg), Ensembl rs1689780791, ESM-1b 1.00, AlphaMissense 0.26, Uncertain significance, Chromosome 2q32-q33 deletion syndrome
- S158G (p.Ser158Gly), cosmic curated COSV99610, ESM-1b 1.00, AlphaMissense 0.32
- C159F (p.Cys159Phe), NCI-TCGA Cosmic COSV5348, cosmic curated COSV53489, ESM-1b 0.00, AlphaMissense 0.31, Variant assessed as somatic; moderate impact.
- C159S (p.Cys159Ser), Ensembl rs2105866015, ESM-1b 1.00, AlphaMissense 0.70
- S160* (p.Ser160Ter), NCI-TCGA Cosmic COSV9961, cosmic curated COSV99611, Variant assessed as somatic; high impact.
- S160P (p.Ser160Pro), NCI-TCGA Cosmic COSV5349, cosmic curated COSV53493, ESM-1b 0.00, AlphaMissense 0.15, Variant assessed as somatic; moderate impact.
- K161R (p.Lys161Arg), rs1360355424, ClinGen CA350388987, ClinVar RCV001034453, gnomAD rs1360355424, REVEL 0.24, ESM-1b 0.41, Benign, Chromosome 2q32-q33 deletion syndrome
- E163K (p.Glu163Lys), NCI-TCGA Cosmic COSV9961, cosmic curated COSV99611, ESM-1b 1.00, AlphaMissense 0.98, Variant assessed as somatic; moderate impact.
Public SATB2 analysis runs
- SATB2 analysis run — SATB2 (1,153 variants) — completed 2026-10-09