Incidental Mutation 'R0372:Nsd2'
ID 30528
Institutional Source Beutler Lab
Gene Symbol Nsd2
Ensembl Gene ENSMUSG00000057406
Gene Name nuclear receptor binding SET domain protein 2
Synonyms 9430010A17Rik, 5830445G22Rik, D030027O06Rik, D930023B08Rik, C130020C13Rik, Whsc1, Whsc1l
MMRRC Submission 038578-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.809) question?
Stock # R0372 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 33978069-34055319 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 34048895 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Leucine at position 1140 (M1140L)
Ref Sequence ENSEMBL: ENSMUSP00000058940 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000058096] [ENSMUST00000066854] [ENSMUST00000075812] [ENSMUST00000137191] [ENSMUST00000139845] [ENSMUST00000202525]
AlphaFold Q8BVE8
Predicted Effect probably damaging
Transcript: ENSMUST00000058096
AA Change: M1140L

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000058940
Gene: ENSMUSG00000057406
AA Change: M1140L

DomainStartEndE-ValueType
low complexity region 12 23 N/A INTRINSIC
PWWP 220 285 3.84e-15 SMART
low complexity region 397 408 N/A INTRINSIC
HMG 452 522 7.64e-9 SMART
low complexity region 532 545 N/A INTRINSIC
low complexity region 629 643 N/A INTRINSIC
PHD 669 711 1.36e-6 SMART
RING 670 710 1.5e1 SMART
PHD 716 763 6.81e-1 SMART
RING 717 762 5.25e-2 SMART
PHD 833 873 2.35e-10 SMART
PWWP 878 940 2.67e-23 SMART
AWS 1011 1062 3.74e-27 SMART
SET 1063 1186 4.48e-43 SMART
PostSET 1187 1203 7.56e-4 SMART
low complexity region 1215 1236 N/A INTRINSIC
PHD 1241 1284 1.98e-8 SMART
low complexity region 1347 1360 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000066854
AA Change: M1141L

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000067205
Gene: ENSMUSG00000057406
AA Change: M1141L

DomainStartEndE-ValueType
low complexity region 12 23 N/A INTRINSIC
PWWP 220 285 3.84e-15 SMART
low complexity region 397 408 N/A INTRINSIC
HMG 452 522 7.64e-9 SMART
low complexity region 532 545 N/A INTRINSIC
low complexity region 630 644 N/A INTRINSIC
PHD 670 712 1.36e-6 SMART
RING 671 711 1.5e1 SMART
PHD 717 764 6.81e-1 SMART
RING 718 763 5.25e-2 SMART
PHD 834 874 2.35e-10 SMART
PWWP 879 941 2.67e-23 SMART
AWS 1012 1063 3.74e-27 SMART
SET 1064 1187 4.48e-43 SMART
PostSET 1188 1204 7.56e-4 SMART
low complexity region 1216 1237 N/A INTRINSIC
PHD 1242 1285 1.98e-8 SMART
low complexity region 1348 1361 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000075812
AA Change: M1141L

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000075210
Gene: ENSMUSG00000057406
AA Change: M1141L

DomainStartEndE-ValueType
low complexity region 12 23 N/A INTRINSIC
PWWP 220 285 3.84e-15 SMART
low complexity region 397 408 N/A INTRINSIC
HMG 452 522 7.64e-9 SMART
low complexity region 532 545 N/A INTRINSIC
low complexity region 630 644 N/A INTRINSIC
PHD 670 712 1.36e-6 SMART
RING 671 711 1.5e1 SMART
PHD 717 764 6.81e-1 SMART
RING 718 763 5.25e-2 SMART
PHD 834 874 2.35e-10 SMART
PWWP 879 941 2.67e-23 SMART
AWS 1012 1063 3.74e-27 SMART
SET 1064 1187 4.48e-43 SMART
PostSET 1188 1204 7.56e-4 SMART
low complexity region 1216 1237 N/A INTRINSIC
PHD 1242 1285 1.98e-8 SMART
low complexity region 1348 1361 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133870
Predicted Effect probably benign
Transcript: ENSMUST00000137191
SMART Domains Protein: ENSMUSP00000122310
Gene: ENSMUSG00000057406

DomainStartEndE-ValueType
low complexity region 12 23 N/A INTRINSIC
Pfam:PWWP 220 332 4.9e-26 PFAM
low complexity region 397 408 N/A INTRINSIC
HMG 452 522 7.64e-9 SMART
low complexity region 532 545 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000139845
SMART Domains Protein: ENSMUSP00000123460
Gene: ENSMUSG00000057406

DomainStartEndE-ValueType
low complexity region 12 23 N/A INTRINSIC
Pfam:PWWP 220 332 4.9e-26 PFAM
low complexity region 397 408 N/A INTRINSIC
HMG 452 522 7.64e-9 SMART
low complexity region 532 545 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000141416
SMART Domains Protein: ENSMUSP00000117233
Gene: ENSMUSG00000057406

DomainStartEndE-ValueType
Pfam:PWWP 202 314 1.1e-25 PFAM
low complexity region 379 390 N/A INTRINSIC
HMG 434 504 4.7e-9 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201572
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200981
Predicted Effect probably benign
Transcript: ENSMUST00000202525
SMART Domains Protein: ENSMUSP00000144255
Gene: ENSMUSG00000057406

DomainStartEndE-ValueType
PHD 11 53 8.5e-9 SMART
RING 12 52 7.3e-2 SMART
PHD 58 105 4.4e-3 SMART
RING 59 104 2.6e-4 SMART
PHD 175 215 1.5e-12 SMART
low complexity region 248 259 N/A INTRINSIC
Meta Mutation Damage Score 0.1822 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 97.9%
  • 10x: 95.2%
  • 20x: 88.6%
Validation Efficiency 97% (70/72)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that contains four domains present in other developmental proteins: a PWWP domain, an HMG box, a SET domain, and a PHD-type zinc finger. It is expressed ubiquitously in early development. Wolf-Hirschhorn syndrome (WHS) is a malformation syndrome associated with a hemizygous deletion of the distal short arm of chromosome 4. This gene maps to the 165 kb WHS critical region and has also been involved in the chromosomal translocation t(4;14)(p16.3;q32.3) in multiple myelomas. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. Some transcript variants are nonsense-mediated mRNA (NMD) decay candidates, hence not represented as reference sequences. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice display reduced fetal size, failed sternum ossification, cleft palate, atrial and ventricular septal defects, stunted growth and postnatal death. Some heterozygotes show severe growth defects, malocclusion, delayed sternum ossification and hypoplasia of the septum secundum. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930578I06Rik T A 14: 64,210,931 (GRCm39) Q99L probably damaging Het
Abca2 A G 2: 25,327,365 (GRCm39) Y641C probably damaging Het
Abhd10 A G 16: 45,557,254 (GRCm39) probably null Het
Acan G T 7: 78,750,349 (GRCm39) A1707S probably benign Het
Ankrd61 T A 5: 143,827,993 (GRCm39) R284S probably benign Het
Ap3d1 T C 10: 80,559,401 (GRCm39) K258E probably damaging Het
Arl6ip6 T G 2: 53,092,933 (GRCm39) F153V probably damaging Het
Atp2c2 C A 8: 120,484,180 (GRCm39) F930L probably benign Het
Avl9 T C 6: 56,703,309 (GRCm39) probably null Het
Axin2 A G 11: 108,814,159 (GRCm39) S16G probably damaging Het
Axin2 T A 11: 108,814,936 (GRCm39) probably benign Het
Bbs7 A T 3: 36,656,981 (GRCm39) D282E probably benign Het
Ccny A T 18: 9,345,201 (GRCm39) V191D probably damaging Het
Cdk11b A G 4: 155,725,957 (GRCm39) probably benign Het
Chd1 T A 17: 17,607,552 (GRCm39) C367S probably benign Het
Cnnm4 G A 1: 36,537,091 (GRCm39) V472M probably damaging Het
Cpb2 T A 14: 75,479,817 (GRCm39) I8N probably benign Het
Dusp11 A G 6: 85,935,712 (GRCm39) probably benign Het
Elmo1 T C 13: 20,756,629 (GRCm39) probably null Het
Gbf1 C T 19: 46,274,143 (GRCm39) P1726S probably benign Het
Hal A G 10: 93,343,415 (GRCm39) probably benign Het
Hlcs T C 16: 93,939,766 (GRCm39) I671V possibly damaging Het
Ifnab A G 4: 88,609,071 (GRCm39) S132P probably benign Het
Ing5 T C 1: 93,740,142 (GRCm39) I70T probably damaging Het
Ints1 T C 5: 139,758,193 (GRCm39) N228S probably damaging Het
Itgb6 T A 2: 60,458,185 (GRCm39) I523F probably benign Het
Kat2b T C 17: 53,945,565 (GRCm39) F328S possibly damaging Het
Kbtbd3 A T 9: 4,316,950 (GRCm39) I34F possibly damaging Het
Klhl11 A T 11: 100,354,348 (GRCm39) I491N probably damaging Het
Lmo7 A T 14: 102,155,489 (GRCm39) probably benign Het
Lrp1 G T 10: 127,428,005 (GRCm39) P523T probably damaging Het
Lrp1b T A 2: 40,620,810 (GRCm39) D3556V probably benign Het
Lrp2 T A 2: 69,365,387 (GRCm39) H262L probably benign Het
Lrrc27 T A 7: 138,806,103 (GRCm39) I256K probably benign Het
Lrrc47 G A 4: 154,104,089 (GRCm39) R523K probably benign Het
Lrrc71 A T 3: 87,653,084 (GRCm39) S111T probably benign Het
Map3k7cl T C 16: 87,378,100 (GRCm39) V72A probably damaging Het
Mphosph10 G T 7: 64,038,603 (GRCm39) probably benign Het
Nlrp4a T C 7: 26,148,657 (GRCm39) probably benign Het
Nt5dc3 T C 10: 86,661,155 (GRCm39) M440T possibly damaging Het
Oog4 A T 4: 143,164,259 (GRCm39) L424Q probably damaging Het
Or5h17 T C 16: 58,820,450 (GRCm39) V134A probably benign Het
Orc5 A T 5: 22,738,782 (GRCm39) Y160N possibly damaging Het
Papola T C 12: 105,785,097 (GRCm39) F410L probably benign Het
Pcdh10 A G 3: 45,333,932 (GRCm39) E82G probably damaging Het
Pcdh20 T C 14: 88,706,439 (GRCm39) Y287C probably damaging Het
Pld1 T A 3: 28,142,787 (GRCm39) probably null Het
Plekha8 G A 6: 54,593,743 (GRCm39) probably null Het
Ppbp C T 5: 90,917,202 (GRCm39) T93M possibly damaging Het
Prpsap2 A G 11: 61,631,826 (GRCm39) I177T possibly damaging Het
Rab3gap2 C T 1: 184,994,891 (GRCm39) T810M possibly damaging Het
Rassf9 A G 10: 102,381,872 (GRCm39) N418S possibly damaging Het
Rnf20 C G 4: 49,650,176 (GRCm39) R582G possibly damaging Het
Serpine2 T C 1: 79,799,147 (GRCm39) I36V probably damaging Het
Sf3b2 C T 19: 5,324,852 (GRCm39) D845N probably damaging Het
Slc24a2 A T 4: 87,145,529 (GRCm39) V175E probably damaging Het
Sned1 T C 1: 93,213,673 (GRCm39) probably benign Het
Snrnp40 C G 4: 130,271,836 (GRCm39) probably null Het
Spg11 GCC G 2: 121,889,928 (GRCm39) probably null Het
Tecrl C T 5: 83,442,506 (GRCm39) C189Y probably damaging Het
Tert A G 13: 73,797,110 (GRCm39) D1116G probably damaging Het
Thnsl2 T C 6: 71,116,774 (GRCm39) Y126C probably damaging Het
Tll2 T C 19: 41,171,752 (GRCm39) probably null Het
Ubqln4 C T 3: 88,463,276 (GRCm39) S147L probably benign Het
Ugt2b5 A T 5: 87,288,117 (GRCm39) C17S probably benign Het
Vps41 A T 13: 19,026,417 (GRCm39) Q505L probably benign Het
Zfp386 T C 12: 116,018,436 (GRCm39) M35T possibly damaging Het
Zfp777 T C 6: 48,021,410 (GRCm39) M71V possibly damaging Het
Zfp938 A T 10: 82,063,662 (GRCm39) L34Q probably damaging Het
Zfp974 A T 7: 27,620,120 (GRCm39) probably null Het
Other mutations in Nsd2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00391:Nsd2 APN 5 34,013,077 (GRCm39) missense probably damaging 1.00
IGL00420:Nsd2 APN 5 34,040,347 (GRCm39) missense possibly damaging 0.82
IGL01343:Nsd2 APN 5 34,000,922 (GRCm39) missense probably damaging 1.00
IGL01403:Nsd2 APN 5 34,042,722 (GRCm39) splice site probably benign
IGL01446:Nsd2 APN 5 34,018,530 (GRCm39) splice site probably benign
IGL01571:Nsd2 APN 5 34,022,031 (GRCm39) missense probably benign 0.32
IGL01862:Nsd2 APN 5 34,001,080 (GRCm39) missense probably null 1.00
IGL02040:Nsd2 APN 5 34,024,915 (GRCm39) splice site probably benign
IGL02528:Nsd2 APN 5 34,036,395 (GRCm39) unclassified probably benign
IGL02553:Nsd2 APN 5 34,003,542 (GRCm39) missense probably damaging 1.00
IGL02799:Nsd2 APN 5 34,022,132 (GRCm39) splice site probably benign
IGL02932:Nsd2 APN 5 34,037,472 (GRCm39) missense probably damaging 1.00
Badminton UTSW 5 34,039,491 (GRCm39) nonsense probably null
Game UTSW 5 34,042,816 (GRCm39) missense probably damaging 1.00
Match UTSW 5 34,036,454 (GRCm39) missense probably damaging 1.00
Navratilova UTSW 5 34,042,834 (GRCm39) missense probably damaging 0.97
Racquet UTSW 5 34,040,189 (GRCm39) missense probably damaging 1.00
serve UTSW 5 34,036,455 (GRCm39) missense possibly damaging 0.95
Tennis UTSW 5 34,000,857 (GRCm39) missense probably damaging 1.00
R0136:Nsd2 UTSW 5 34,012,880 (GRCm39) missense possibly damaging 0.89
R0521:Nsd2 UTSW 5 34,000,682 (GRCm39) missense probably damaging 1.00
R0548:Nsd2 UTSW 5 34,050,882 (GRCm39) missense probably damaging 1.00
R0726:Nsd2 UTSW 5 34,018,372 (GRCm39) unclassified probably benign
R1018:Nsd2 UTSW 5 34,000,585 (GRCm39) missense probably damaging 1.00
R1638:Nsd2 UTSW 5 34,039,464 (GRCm39) missense possibly damaging 0.87
R1649:Nsd2 UTSW 5 34,011,984 (GRCm39) missense probably damaging 0.98
R1675:Nsd2 UTSW 5 34,018,493 (GRCm39) missense probably benign 0.04
R1900:Nsd2 UTSW 5 34,003,513 (GRCm39) missense probably benign
R2001:Nsd2 UTSW 5 34,000,746 (GRCm39) missense probably damaging 1.00
R2167:Nsd2 UTSW 5 34,040,263 (GRCm39) missense probably damaging 1.00
R2261:Nsd2 UTSW 5 34,042,871 (GRCm39) missense probably damaging 1.00
R2966:Nsd2 UTSW 5 34,003,466 (GRCm39) missense probably benign 0.01
R3931:Nsd2 UTSW 5 34,003,461 (GRCm39) missense probably benign 0.01
R4429:Nsd2 UTSW 5 34,000,546 (GRCm39) missense probably damaging 1.00
R4596:Nsd2 UTSW 5 34,040,262 (GRCm39) missense probably damaging 1.00
R4958:Nsd2 UTSW 5 34,049,366 (GRCm39) missense probably damaging 1.00
R5346:Nsd2 UTSW 5 34,036,480 (GRCm39) missense possibly damaging 0.94
R5957:Nsd2 UTSW 5 34,012,947 (GRCm39) missense probably damaging 1.00
R6054:Nsd2 UTSW 5 34,039,505 (GRCm39) missense probably damaging 1.00
R6124:Nsd2 UTSW 5 34,000,610 (GRCm39) missense probably benign 0.08
R6302:Nsd2 UTSW 5 34,024,921 (GRCm39) missense possibly damaging 0.93
R6390:Nsd2 UTSW 5 34,038,525 (GRCm39) missense probably damaging 1.00
R6496:Nsd2 UTSW 5 34,000,857 (GRCm39) missense probably damaging 1.00
R6828:Nsd2 UTSW 5 34,050,912 (GRCm39) missense probably damaging 0.98
R6925:Nsd2 UTSW 5 34,036,454 (GRCm39) missense probably damaging 1.00
R7148:Nsd2 UTSW 5 34,042,855 (GRCm39) missense possibly damaging 0.57
R7311:Nsd2 UTSW 5 34,049,380 (GRCm39) missense probably damaging 1.00
R7337:Nsd2 UTSW 5 34,042,816 (GRCm39) missense probably damaging 1.00
R7466:Nsd2 UTSW 5 34,039,491 (GRCm39) nonsense probably null
R7567:Nsd2 UTSW 5 34,003,570 (GRCm39) missense probably damaging 0.99
R7704:Nsd2 UTSW 5 34,028,811 (GRCm39) makesense probably null
R7822:Nsd2 UTSW 5 34,000,938 (GRCm39) missense probably damaging 0.97
R7939:Nsd2 UTSW 5 34,012,933 (GRCm39) missense probably benign 0.22
R8127:Nsd2 UTSW 5 34,042,834 (GRCm39) missense probably damaging 0.97
R8485:Nsd2 UTSW 5 34,040,189 (GRCm39) missense probably damaging 1.00
R8782:Nsd2 UTSW 5 34,000,485 (GRCm39) start codon destroyed probably benign
R8783:Nsd2 UTSW 5 34,036,455 (GRCm39) missense possibly damaging 0.95
R8845:Nsd2 UTSW 5 34,039,885 (GRCm39) missense probably damaging 1.00
R9034:Nsd2 UTSW 5 34,037,478 (GRCm39) missense possibly damaging 0.92
R9183:Nsd2 UTSW 5 34,028,796 (GRCm39) missense probably damaging 0.99
R9283:Nsd2 UTSW 5 34,001,058 (GRCm39) missense probably benign 0.34
R9438:Nsd2 UTSW 5 34,000,632 (GRCm39) missense probably damaging 0.99
R9486:Nsd2 UTSW 5 34,018,493 (GRCm39) missense probably benign 0.04
R9792:Nsd2 UTSW 5 34,003,489 (GRCm39) missense possibly damaging 0.89
R9793:Nsd2 UTSW 5 34,003,489 (GRCm39) missense possibly damaging 0.89
R9795:Nsd2 UTSW 5 34,003,489 (GRCm39) missense possibly damaging 0.89
X0020:Nsd2 UTSW 5 34,012,101 (GRCm39) missense probably damaging 1.00
Z1088:Nsd2 UTSW 5 34,013,082 (GRCm39) critical splice donor site probably null
Z1177:Nsd2 UTSW 5 34,012,864 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCGTGTCAGCACAGCATCAGCATC -3'
(R):5'- CAGGCACACAGTGGCATAACTCAG -3'

Sequencing Primer
(F):5'- AGGAGTTGATACCGCTTGCC -3'
(R):5'- CAGTGGCATAACTCAGAGATTCATC -3'
Posted On 2013-04-24