Incidental Mutation 'R5346:Nsd2'
ID 422606
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 042925-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.809) question?
Stock # R5346 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 33978069-34055319 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 34036480 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 655 (S655T)
Ref Sequence ENSEMBL: ENSMUSP00000075210 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000058096] [ENSMUST00000066854] [ENSMUST00000075812] [ENSMUST00000114399] [ENSMUST00000137191] [ENSMUST00000139845] [ENSMUST00000202525]
AlphaFold Q8BVE8
Predicted Effect possibly damaging
Transcript: ENSMUST00000058096
AA Change: S654T

PolyPhen 2 Score 0.873 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000058940
Gene: ENSMUSG00000057406
AA Change: S654T

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 possibly damaging
Transcript: ENSMUST00000066854
AA Change: S655T

PolyPhen 2 Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000067205
Gene: ENSMUSG00000057406
AA Change: S655T

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 possibly damaging
Transcript: ENSMUST00000075812
AA Change: S655T

PolyPhen 2 Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000075210
Gene: ENSMUSG00000057406
AA Change: S655T

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 benign
Transcript: ENSMUST00000114399
SMART Domains Protein: ENSMUSP00000110041
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: 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: ENSMUST00000202912
Predicted Effect probably benign
Transcript: ENSMUST00000142080
SMART Domains Protein: ENSMUSP00000115251
Gene: ENSMUSG00000057406

DomainStartEndE-ValueType
Blast:SET 2 148 7e-47 BLAST
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
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.8%
  • 10x: 97.7%
  • 20x: 96.3%
Validation Efficiency
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arap2 T A 5: 62,872,089 (GRCm39) Y513F probably benign Het
Cluh C A 11: 74,556,044 (GRCm39) H832N probably damaging Het
Cntfr G T 4: 41,675,042 (GRCm39) Y21* probably null Het
Cog2 T C 8: 125,273,370 (GRCm39) S570P possibly damaging Het
Cops7b A G 1: 86,510,790 (GRCm39) probably benign Het
Cpox G A 16: 58,495,649 (GRCm39) G322D probably damaging Het
Dop1a A G 9: 86,402,835 (GRCm39) D1345G probably damaging Het
Dqx1 G A 6: 83,036,700 (GRCm39) D235N possibly damaging Het
Dscaml1 A G 9: 45,361,857 (GRCm39) I206V possibly damaging Het
Ednra T C 8: 78,401,597 (GRCm39) Y231C probably damaging Het
Ehhadh T C 16: 21,581,540 (GRCm39) Y484C probably damaging Het
Fmnl3 A T 15: 99,229,871 (GRCm39) V150D probably damaging Het
Gabrb2 T A 11: 42,312,216 (GRCm39) S14T probably benign Het
Gm10608 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 9: 118,989,792 (GRCm39) probably null Het
Gpatch2 T C 1: 186,958,065 (GRCm39) L140P probably benign Het
Gsdmc A G 15: 63,648,735 (GRCm39) Y400H probably damaging Het
Heatr5b A G 17: 79,135,415 (GRCm39) S239P probably benign Het
Hmcn1 A T 1: 150,498,995 (GRCm39) I4004N probably damaging Het
Insc T A 7: 114,403,776 (GRCm39) N63K possibly damaging Het
Mmp28 T C 11: 83,333,489 (GRCm39) H484R probably benign Het
Nptn C A 9: 58,531,070 (GRCm39) Y64* probably null Het
Nub1 A G 5: 24,902,414 (GRCm39) E253G probably damaging Het
Or3a1d T C 11: 74,237,496 (GRCm39) R305G probably benign Het
Pde3b T A 7: 114,105,425 (GRCm39) H452Q probably benign Het
Pkhd1 T C 1: 20,462,321 (GRCm39) M2078V probably benign Het
Pkhd1 T C 1: 20,593,658 (GRCm39) D1485G probably damaging Het
Pkhd1l1 A C 15: 44,404,363 (GRCm39) T2331P probably damaging Het
Plk5 G A 10: 80,198,942 (GRCm39) G433E probably damaging Het
Pnliprp2 T A 19: 58,748,232 (GRCm39) D4E probably benign Het
Prag1 A G 8: 36,570,839 (GRCm39) D474G probably damaging Het
Psmc1 A G 12: 100,086,359 (GRCm39) N332S probably damaging Het
Rad9a G C 19: 4,251,517 (GRCm39) probably null Het
Slf1 A G 13: 77,240,490 (GRCm39) V396A probably benign Het
Stat6 G A 10: 127,488,182 (GRCm39) R312K probably benign Het
Tgm1 A T 14: 55,948,629 (GRCm39) V174E probably damaging Het
Tnc A G 4: 63,926,892 (GRCm39) V878A probably benign Het
Ube4b A T 4: 149,421,881 (GRCm39) H969Q possibly damaging Het
Ubr4 T C 4: 139,155,802 (GRCm39) I2209T probably damaging Het
Ulk2 A C 11: 61,725,740 (GRCm39) L112R probably damaging Het
Wdr35 T C 12: 9,028,684 (GRCm39) Y101H probably benign Het
Xpo7 A G 14: 70,921,117 (GRCm39) L617P probably damaging 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
R0372:Nsd2 UTSW 5 34,048,895 (GRCm39) missense probably damaging 0.98
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
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'- TTAATTCCAAAGCCAGTGATGGTG -3'
(R):5'- AATTCTGCTGACAGTCTAACCC -3'

Sequencing Primer
(F):5'- CCAAAGCCAGTGATGGTGTATATC -3'
(R):5'- CCTTCCAAAGAGGTATCCGTGAG -3'
Posted On 2016-08-04