NIPBL (Nipped-B-like protein) variants and mutations
NIPBL (also known as Nipped-B-like protein) is a human protein-coding gene encoding a nipped-B-like protein. A cohesin-loading factor that helps place the cohesin complex onto DNA. Pathogenic variants are a major cause of Cornelia de Lange syndrome. This analysis covers 2,510 NIPBL variants and mutations. Of these, 92% have computational variant effect predictions. Disease context includes Cornelia de Lange syndrome, hereditary disease, and Dislocated radial head. Example NIPBL variants include M1I, M1K, and N2S.
Variant analysis overview
- Gene: NIPBL
- Protein: Nipped-B-like protein
- UniProt accession: Q6KC79
- Organism: Homo sapiens
- Variants analyzed: 2510
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 2,542 unspecified-consequence records; 122 missense variants; 88 synonymous variants; 3 in-frame deletions; 1 in-frame insertions; 5 splice-region variants; 3 substitution
- Prediction scores: 2,297 variants have prediction scores (92% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Cornelia de Lange syndrome, hereditary disease, Dislocated radial head, Intellectual disability, low grade glioma, microcephaly, cleft palate, Abnormal brain morphology, Tetralogy of Fallot, septic shock, Myoclonus, liver disorder.
Protein structure and variant hotspots
- Protein features: 36 post-translational modification sites.
- PTM context: 27 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 NIPBL
Notable NIPBL variants
Examples include M1I, M1K, N2S, G3R, G3E, G3G, D4V, D4H. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1I (p.Met1Ile), rs587783937, ClinGen CA272094, ClinVar RCV000146596, ESM-1b 0.77, AlphaMissense 0.99, Pathogenic, Cornelia de Lange syndrome 1
- M1K (p.Met1Lys), rs121918264, ClinGen CA252112, ClinVar RCV000002221, ClinVar RCV004700178, ESM-1b 0.64, AlphaMissense 0.99, Pathogenic/Likely pathogenic, not provided; Cornelia de Lange syndrome 1
- N2S (p.Asn2Ser), rs1458071910, ClinGen CA359473447, ClinVar RCV002904736, TOPMed rs1458071910, REVEL 0.65, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- G3R (p.Gly3Arg), gnomAD 5-36953703-G-A, REVEL 0.53, ESM-1b 0.00
- G3E (p.Gly3Glu), gnomAD 5-36953704-G-A, REVEL 0.65, ESM-1b 0.00
- G3G (p.Gly3Gly), gnomAD 5-36953705-G-A, CADD 11.30
- D4V (p.Asp4Val), TOPMed rs983690389, ESM-1b 0.00, AlphaMissense 1.00
- D4H (p.Asp4His), gnomAD 5-36953706-G-C, REVEL 0.70, ESM-1b 0.00
- D4N (p.Asp4Asn), gnomAD 5-36953706-G-A, REVEL 0.67, ESM-1b 0.00
- M5R (p.Met5Arg), ExAC rs764272515, TOPMed rs764272515, gnomAD rs764272515, REVEL 0.61, ESM-1b 0.00
- M5T (p.Met5Thr), ExAC rs764272515, TOPMed rs764272515, gnomAD rs764272515, ESM-1b 0.00, AlphaMissense 0.99
- M5V (p.Met5Val), rs1400551368, NCI-TCGA Cosmic COSV5694, cosmic curated COSV56942, gnomAD rs1400551368, REVEL 0.48, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- M5I (p.Met5Ile), gnomAD 5-36953711-G-A, REVEL 0.46, ESM-1b 0.00
- P6P (p.Pro6Pro), gnomAD 5-36953714-C-A, CADD 11.70
- H7P (p.His7Pro), gnomAD 5-36953716-A-C, REVEL 0.68, ESM-1b 0.00
- P9A (p.Pro9Ala), gnomAD 5-36953721-C-G, REVEL 0.77, ESM-1b 0.00
- T12T (p.Thr12Thr), rs1740649844, gnomAD 5-36953732-T-C, CADD 12.70
- L13L (p.Leu13Leu), rs1740650095, gnomAD 5-36953735-T-C, CADD 11.50
- A14G (p.Ala14Gly), gnomAD 5-36953737-C-G, REVEL 0.71, ESM-1b 0.00
- A14A (p.Ala14Ala), rs727504045, gnomAD 5-36953738-G-C, CADD 11.70
- G15R (p.Gly15Arg), UniProt VAR 072996, ESM-1b 0.00, AlphaMissense 1.00, Pathogenic/Likely pathogenic, not provided; Cornelia de Lange syndrome 1
- G15T (p.Gly15Thr), NCI-TCGA Cosmic COSV9924, cosmic curated COSV99242, Variant assessed as somatic; moderate impact.
- G15G (p.Gly15Gly), rs757439561, gnomAD 5-36953741-G-C, CADD 11.00
- I16I (p.Ile16Ile), rs1416136879, gnomAD 5-36953744-T-C, CADD 11.80
- A17T (p.Ala17Thr), NCI-TCGA Cosmic COSV5696, NCI-TCGA Cosmic COSV9923, cosmic curated COSV99238, Variant assessed as somatic; moderate impact.
- A17G (p.Ala17Gly), gnomAD 5-36953746-C-G, REVEL 0.55, ESM-1b 0.00
- S18G (p.Ser18Gly), gnomAD rs1286357184, REVEL 0.54, ESM-1b 0.00
- S18R (p.Ser18Arg), gnomAD 5-36953750-T-G, REVEL 0.59, ESM-1b 0.00
- L19V (p.Leu19Val), gnomAD 5-36953751-C-G, REVEL 0.62, ESM-1b 0.00
- D21E (p.Asp21Glu), gnomAD rs1740652106, REVEL 0.68, ESM-1b 0.00
- L22F (p.Leu22Phe), TOPMed rs1580319373, gnomAD rs1580319373, REVEL 0.65, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- L23L (p.Leu23Leu), gnomAD 5-36955476-G-T, CADD 10.30
- N24D (p.Asn24Asp), ExAC rs775499754, gnomAD rs775499754, ESM-1b 0.00, AlphaMissense 0.97
- N24T (p.Asn24Thr), Ensembl rs1580322773, ESM-1b 0.00, AlphaMissense 0.92
- Q25* (p.Gln25Ter), rs2478986417, ClinGen CA359473751, ClinVar RCV003404183, Likely pathogenic
- P27L (p.Pro27Leu), gnomAD 5-36955487-C-T, REVEL 0.83, ESM-1b 0.00
- L28L (p.Leu28Leu), gnomAD 5-36955491-T-C, CADD 9.40
- P29Q (p.Pro29Gln), UniProt VAR 072997, ESM-1b 0.00, AlphaMissense 1.00, Pathogenic, in CDLS1
- P29S (p.Pro29Ser), Ensembl rs1740837139, ESM-1b 0.00, AlphaMissense 0.99
- P29P (p.Pro29Pro), rs587784061, gnomAD 5-36955494-A-G, CADD 10.80
- S30S (p.Ser30Ser), rs1329131567, gnomAD 5-36955497-T-A, CADD 11.00
- P31S (p.Pro31Ser), gnomAD 5-36955498-C-T, REVEL 0.53, ESM-1b 0.00
- P31P (p.Pro31Pro), gnomAD 5-36955500-T-C, CADD 11.40
- L32L (p.Leu32Leu), gnomAD 5-36955501-T-C, CADD 11.00
- P33S (p.Pro33Ser), gnomAD 5-36955504-C-T, REVEL 0.66, ESM-1b 0.00
- P33T (p.Pro33Thr), gnomAD 5-36955504-C-A, REVEL 0.71, ESM-1b 0.00
- P33P (p.Pro33Pro), gnomAD 5-36955506-T-G, CADD 12.60
- A34V (p.Ala34Val), gnomAD 5-36955508-C-T, REVEL 0.59, ESM-1b 0.00
- T35A (p.Thr35Ala), rs763015442, ClinGen CA3235742, ClinVar RCV003879669, ExAC rs763015442, REVEL 0.61, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- T35I (p.Thr35Ile), gnomAD 5-36955511-C-T, REVEL 0.72, ESM-1b 0.00
- T35T (p.Thr35Thr), rs1350258771, gnomAD 5-36955512-A-G, CADD 8.76
- T36T (p.Thr36Thr), gnomAD 5-36955515-T-C, CADD 11.40
- T37A (p.Thr37Ala), rs892645096, gnomAD 5-36955516-A-G, REVEL 0.40, ESM-1b 0.00
- T37T (p.Thr37Thr), rs576203422, gnomAD 5-36955518-A-G, CADD 10.70
- K38E (p.Lys38Glu), TOPMed rs1286814983, gnomAD rs1286814983, REVEL 0.63, ESM-1b 0.00
- S39S (p.Ser39Ser), rs1740839785, gnomAD 5-36955524-C-T, CADD 11.50
- L40V (p.Leu40Val), TOPMed rs1740840042, ESM-1b 0.00, AlphaMissense 0.73
- L40F (p.Leu40Phe), gnomAD 5-36955525-C-T, REVEL 0.68, ESM-1b 0.00
- L41L (p.Leu41Leu), rs774269226, gnomAD 5-36955530-C-T, CADD 7.03
- F42C (p.Phe42Cys), gnomAD 5-36955532-T-G, REVEL 0.77, ESM-1b 0.00
- F42F (p.Phe42Phe), rs727504046, gnomAD 5-36955533-T-C, CADD 11.10
- A44A (p.Ala44Ala), gnomAD 5-36955539-A-G, CADD 11.00
- R45* (p.Arg45Ter), rs80358367, ClinGen CA267522, cosmic curated COSV56963, ClinVar RCV000086366, Pathogenic
- R45Q (p.Arg45Gln), rs1290230112, ClinGen CA359474063, NCI-TCGA Cosmic COSV5694, cosmic curated COSV56949, REVEL 0.74, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- R45G (p.Arg45Gly), gnomAD 5-36955540-C-G, REVEL 0.80, ESM-1b 0.00
- R45P (p.Arg45Pro), gnomAD 5-36955541-G-C, REVEL 0.89, ESM-1b 0.00
- A47A (p.Ala47Ala), gnomAD 5-36955548-A-T, CADD 12.20
- E48E (p.Glu48Glu), gnomAD 5-36955551-A-G, CADD 11.70
- E49* (p.Glu49Ter), rs587783886, ClinGen CA271971, ClinVar RCV000146520, Ensembl rs587783886, Pathogenic
- V50G (p.Val50Gly), TOPMed rs1740841745, ESM-1b 0.00, AlphaMissense 0.88, Uncertain significance, Inborn genetic diseases; Cornelia de Lange syndrome 1
- V50V (p.Val50Val), rs767626703, gnomAD 5-36955557-G-A, CADD 10.10
- N51N (p.Asn51Asn), rs1265934818, gnomAD 5-36955560-C-T, CADD 9.34
- C52A (p.Cys52Ala), NCI-TCGA Cosmic COSV9924, cosmic curated COSV99242, TOPMed rs892645096, Variant assessed as somatic; moderate impact.
- L54* (p.Leu54Ter), rs1740842785, ClinGen CA359474218, ClinVar RCV001195989, Ensembl rs1740842785, Pathogenic
- L54L (p.Leu54Leu), gnomAD 5-36955567-T-C, CADD 10.30
- A55T (p.Ala55Thr), rs2478987011, ClinGen CA359474230, ClinVar RCV003602554, ESM-1b 0.00, AlphaMissense 0.11, Uncertain significance, Cornelia de Lange syndrome 1
- A55V (p.Ala55Val), TOPMed rs1740843039, gnomAD rs1740843039, REVEL 0.29, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- A55G (p.Ala55Gly), NCI-TCGA Cosmic COSV5695, cosmic curated COSV56953, Variant assessed as somatic; moderate impact.
- A55S (p.Ala55Ser), gnomAD 5-36955570-G-T, REVEL 0.22, ESM-1b 0.00
- C56R (p.Cys56Arg), gnomAD rs1451376095, REVEL 0.59, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- C56G (p.Cys56Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- C56A (p.Cys56Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- C56Y (p.Cys56Tyr), gnomAD 5-36955574-G-A, REVEL 0.78, ESM-1b 0.00
- R57G (p.Arg57Gly), rs539552810, ClinGen CA117021532, ClinVar RCV002922090, 1000Genomes rs539552810, REVEL 0.82, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases; Cornelia de Lange syndrome 1
- R57T (p.Arg57Thr), ExAC rs756415457, gnomAD rs756415457, REVEL 0.86, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- R57K (p.Arg57Lys), gnomAD 5-36955577-G-A, REVEL 0.64, ESM-1b 0.00
- D59G (p.Asp59Gly), ExAC rs766738333, gnomAD rs766738333, REVEL 0.48, ESM-1b 0.00
- D59D (p.Asp59Asp), rs2149599551, gnomAD 5-36955584-C-T, CADD 9.75
- N60I (p.Asn60Ile), 1000Genomes rs142703446, ESP rs142703446, ExAC rs142703446, TOPMed rs142703446, REVEL 0.38, ESM-1b 0.00, Benign
- N60S (p.Asn60Ser), rs142703446, ClinGen CA3235749, cosmic curated COSV56955, ClinVar RCV000284905, REVEL 0.23, ESM-1b 0.00, Benign/Likely benign, Inborn genetic diseases; not specified; NIPBL-related disorder
- N60T (p.Asn60Thr), 1000Genomes rs142703446, ESP rs142703446, ExAC rs142703446, TOPMed rs142703446, REVEL 0.24, ESM-1b 0.00, Benign
- V62L (p.Val62Leu), rs2478987184, ClinGen CA359474352, ClinVar RCV002841068, ClinVar RCV005036566, ESM-1b 0.00, AlphaMissense 0.73, Uncertain significance, Cornelia de Lange syndrome 1; Inborn genetic diseases
- S63* (p.Ser63Ter), rs1740845459, ClinGen CA359474373, ClinVar RCV001089569, Ensembl rs1740845459, Pathogenic
- S63S (p.Ser63Ser), rs755503212, gnomAD 5-36955596-A-C, CADD 11.00
- Q64H (p.Gln64His), Ensembl rs769022116, REVEL 0.61, ESM-1b 0.00, Uncertain significance, not provided
- Q64K (p.Gln64Lys), gnomAD 5-36955597-C-A, REVEL 0.81, ESM-1b 0.00
- L65P (p.Leu65Pro), rs2478987276, ClinGen CA359474409, ClinVar RCV003604203, ESM-1b 0.00, AlphaMissense 1.00, Uncertain significance, Cornelia de Lange syndrome 1
- L65R (p.Leu65Arg), rs2478987276, ClinGen CA359474406, ClinVar RCV003131805, ESM-1b 0.00, AlphaMissense 1.00, Uncertain significance, Cornelia de Lange syndrome 1
- L65V (p.Leu65Val), rs925563626, ClinGen CA117021547, ClinVar RCV003604520, TOPMed rs925563626, REVEL 0.73, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- L65I (p.Leu65Ile), gnomAD 5-36955600-C-A, REVEL 0.68, ESM-1b 0.00
- V66A (p.Val66Ala), gnomAD rs1429907906, ESM-1b 0.00, AlphaMissense 0.57, Uncertain significance, not provided
- V66V (p.Val66Val), rs146033170, gnomAD 5-36955605-C-G, CADD 8.96
- H67R (p.His67Arg), rs1388552505, ClinGen CA359474439, ClinVar RCV002214352, ClinVar RCV005032189, REVEL 0.63, ESM-1b 0.00, Uncertain significance, not provided; Cornelia de Lange syndrome 1
- H67H (p.His67His), gnomAD 5-36955608-T-C, CADD 8.24
- S68G (p.Ser68Gly), TOPMed rs1740847769, REVEL 0.40, ESM-1b 0.00
- S68N (p.Ser68Asn), gnomAD rs1386162274, REVEL 0.44, ESM-1b 0.00
- S68S (p.Ser68Ser), rs746472461, gnomAD 5-36955611-C-T, CADD 11.00
- L69P (p.Leu69Pro), rs587783895, ClinGen CA271995, ClinVar RCV000146534, Ensembl rs587783895, ESM-1b 0.00, AlphaMissense 1.00, Likely pathogenic, Cornelia de Lange syndrome 1
- L69V (p.Leu69Val), Ensembl rs776899302, REVEL 0.70, ESM-1b 0.00
- L69L (p.Leu69Leu), rs1294399604, gnomAD 5-36955614-C-G, CADD 9.38
- N70I (p.Asn70Ile), UniProt VAR 072998, ESM-1b 0.00, AlphaMissense 0.82, Pathogenic, in CDLS1
- N70K (p.Asn70Lys), rs756859262, ClinGen CA3235752, cosmic curated COSV10940, ClinVar RCV002843271, REVEL 0.36, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- N70S (p.Asn70Ser), rs2149599601, ClinGen CA359474468, ClinVar RCV001732844, ClinVar RCV002488497, REVEL 0.28, ESM-1b 0.00, Uncertain significance, not provided; Cornelia de Lange syndrome 1
- N70N (p.Asn70Asn), gnomAD 5-36955617-C-T, CADD 10.30
- Q71E (p.Gln71Glu), rs780649689, ExAC rs780649689, gnomAD rs780649689, REVEL 0.62, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- Q71H (p.Gln71His), gnomAD rs988335122, REVEL 0.61, ESM-1b 0.00
- Q71R (p.Gln71Arg), gnomAD 5-36955619-A-G, REVEL 0.52, ESM-1b 0.00
- V72A (p.Val72Ala), rs2478987527, ClinGen CA359474482, ClinVar RCV002467019, REVEL 0.60, ESM-1b 0.00, Uncertain significance, not provided
- V72L (p.Val72Leu), gnomAD 5-36955621-G-T, REVEL 0.54, ESM-1b 0.00
- S73L (p.Ser73Leu), UniProt VAR 072999, ESM-1b 0.00, AlphaMissense 0.88, Uncertain significance, in CDLS1
- T74S (p.Thr74Ser), gnomAD 5-36955627-A-T, REVEL 0.54, ESM-1b 0.00
- T74I (p.Thr74Ile), gnomAD 5-36955628-C-T, REVEL 0.72, ESM-1b 0.00
- D75E (p.Asp75Glu), gnomAD 5-36955632-T-G, REVEL 0.35, ESM-1b 0.00
- D75D (p.Asp75Asp), rs745537254, gnomAD 5-36955632-T-C, CADD 11.00
- H76D (p.His76Asp), TOPMed rs1387690193, gnomAD rs1387690193, REVEL 0.86, ESM-1b 0.00
- H76Q (p.His76Gln), Ensembl rs74401909, ESM-1b 0.00, AlphaMissense 0.96
- H76P (p.His76Pro), gnomAD 5-36955634-A-C, REVEL 0.89, ESM-1b 0.00
- I77V (p.Ile77Val), Ensembl rs376938430, REVEL 0.65, ESM-1b 0.00
- I77T (p.Ile77Thr), gnomAD 5-36955637-T-C, REVEL 0.88, ESM-1b 0.00
- E78E (p.Glu78Glu), gnomAD 5-36958107-G-A, CADD 4.27
- D81N (p.Asp81Asn), gnomAD 5-36958114-G-A, REVEL 0.68, ESM-1b 0.00
- N82D (p.Asn82Asp), gnomAD rs1741184137, REVEL 0.67, ESM-1b 0.00
- L83F (p.Leu83Phe), gnomAD rs1741184454, REVEL 0.42, ESM-1b 0.00
- G84A (p.Gly84Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G84S (p.Gly84Ser), rs369249480, ClinGen CA3235770, ClinVar RCV003072975, ESP rs369249480, REVEL 0.51, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- G84D (p.Gly84Asp), gnomAD 5-36958124-G-A, REVEL 0.55, ESM-1b 0.00
- G84G (p.Gly84Gly), rs1206531048, gnomAD 5-36958125-C-T, CADD 15.00
- S85T (p.Ser85Thr), gnomAD rs1253388106, REVEL 0.46, ESM-1b 0.00
- S85S (p.Ser85Ser), rs765659128, gnomAD 5-36958128-T-C, CADD 11.60
- D86N (p.Asp86Asn), rs1188531884, ClinGen CA16609631, ClinVar RCV002777412, gnomAD rs1188531884, REVEL 0.57, ESM-1b 0.00, Likely benign, Inborn genetic diseases
- D86A (p.Asp86Ala), gnomAD 5-36958130-A-C, REVEL 0.69, ESM-1b 0.00
- D86G (p.Asp86Gly), gnomAD 5-36958130-A-G, REVEL 0.69, ESM-1b 0.00
- D87G (p.Asp87Gly), cosmic curated COSV10959, Ensembl rs2149602894, ESM-1b 0.00, AlphaMissense 0.96
- P88S (p.Pro88Ser), ExAC rs753307330, TOPMed rs753307330, gnomAD rs753307330, REVEL 0.55, ESM-1b 0.00
- P88A (p.Pro88Ala), gnomAD 5-36958135-C-G, REVEL 0.53, ESM-1b 0.00
- P88L (p.Pro88Leu), gnomAD 5-36958136-C-T, REVEL 0.53, ESM-1b 0.00
- P88P (p.Pro88Pro), gnomAD 5-36958137-A-T, CADD 7.66
- E89K (p.Glu89Lys), rs1000583856, ClinGen CA117022594, ClinVar RCV003414427, ClinVar RCV004961279, ESM-1b 0.00, AlphaMissense 0.96, Uncertain significance, NIPBL-related disorder; Inborn genetic diseases
- E89del (p.Glu89del), rs1741186913, gnomAD 5-36958136-CAGA-C, CADD 22.20
- E89G (p.Glu89Gly), gnomAD 5-36958139-A-G, REVEL 0.58, ESM-1b 0.00
- E89E (p.Glu89Glu), rs1204393071, gnomAD 5-36958140-A-G, CADD 13.30
- G90C (p.Gly90Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- p.Asp91dup, gnomAD 5-36958143-T-TGAC, CADD 20.60
- D91D (p.Asp91Asp), rs1269255544, gnomAD 5-36958146-C-T, CADD 7.52
- I92T (p.Ile92Thr), ExAC rs780783113, gnomAD rs780783113, REVEL 0.31, ESM-1b 0.00
- I92V (p.Ile92Val), ESP rs373268240, ExAC rs373268240, TOPMed rs373268240, gnomAD rs373268240, REVEL 0.18, ESM-1b 0.00, Likely benign, Inborn genetic diseases
- P93S (p.Pro93Ser), ExAC rs750047678, gnomAD rs750047678, REVEL 0.75, ESM-1b 0.00
- V94D (p.Val94Asp), TOPMed rs1741188824, ESM-1b 0.00, AlphaMissense 0.83
- V94I (p.Val94Ile), gnomAD 5-36958153-G-A, REVEL 0.34, ESM-1b 0.00
- V94V (p.Val94Val), gnomAD 5-36958155-C-T, CADD 10.60
- L95L (p.Leu95Leu), gnomAD 5-36958158-G-A, CADD 9.12
- L96F (p.Leu96Phe), gnomAD 5-36958161-G-T, REVEL 0.70, ESM-1b 0.00
- Q97Q (p.Gln97Gln), rs1741189318, gnomAD 5-36958164-G-A, CADD 8.95
- A98D (p.Ala98Asp), Ensembl rs1741189550, ESM-1b 0.00, AlphaMissense 0.92
- A98A (p.Ala98Ala), rs142184978, gnomAD 5-36958167-C-T, CADD 6.58
- V99I (p.Val99Ile), rs779888500, ClinGen CA3235776, ClinVar RCV002908961, ExAC rs779888500, REVEL 0.17, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- V99L (p.Val99Leu), ExAC rs779888500, TOPMed rs779888500, gnomAD rs779888500, ESM-1b 0.00, AlphaMissense 0.35, Uncertain significance
- V99F (p.Val99Phe), gnomAD 5-36958168-G-T, REVEL 0.53, ESM-1b 0.00
- L100L (p.Leu100Leu), rs768550843, gnomAD 5-36958173-G-A, CADD 10.10
- A101G (p.Ala101Gly), TOPMed rs986024813, gnomAD rs986024813, REVEL 0.23, ESM-1b 0.00, Uncertain significance
- A101V (p.Ala101Val), TOPMed rs986024813, gnomAD rs986024813, REVEL 0.46, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1
- A101C (p.Ala101Cys), NCI-TCGA Cosmic COSV5694, cosmic curated COSV56946, Variant assessed as somatic; moderate impact.
- A101S (p.Ala101Ser), gnomAD 5-36958174-G-T, REVEL 0.30, ESM-1b 0.00
- A101T (p.Ala101Thr), gnomAD 5-36958174-G-A, REVEL 0.33, ESM-1b 0.00
- R102S (p.Arg102Ser), rs778661285, ClinGen CA3235779, ClinVar RCV002444328, ClinVar RCV003130717, REVEL 0.77, ESM-1b 0.00, Uncertain significance, Cornelia de Lange syndrome 1; Inborn genetic diseases
- R102del (p.Arg102del), gnomAD 5-36958175-CAAG-C, CADD 20.60
- S103T (p.Ser103Thr), ExAC rs748123160, gnomAD rs748123160, REVEL 0.30, ESM-1b 0.00, Uncertain significance, NIPBL-related disorder
- S103G (p.Ser103Gly), gnomAD 5-36958180-A-G, REVEL 0.27, ESM-1b 0.00
- S103N (p.Ser103Asn), gnomAD 5-36958181-G-A, REVEL 0.39, ESM-1b 0.00
- P104A (p.Pro104Ala), rs772009624, ClinGen CA3235781, ClinVar RCV001868356, ClinVar RCV002318083, REVEL 0.85, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases; Cornelia de Lange syndrome 1
Public NIPBL analysis runs
- NIPBL analysis run — NIPBL (2,510 variants) — completed 2026-10-09