Incidental Mutation 'R0652:Nsd1'
ID 62329
Institutional Source Beutler Lab
Gene Symbol Nsd1
Ensembl Gene ENSMUSG00000021488
Gene Name nuclear receptor-binding SET-domain protein 1
Synonyms KMT3B
MMRRC Submission 038837-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0652 (G1)
Quality Score 214
Status Not validated
Chromosome 13
Chromosomal Location 55357595-55466138 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 55395399 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 1000 (D1000G)
Ref Sequence ENSEMBL: ENSMUSP00000153677 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000099490] [ENSMUST00000224973]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000099490
AA Change: D1103G

PolyPhen 2 Score 0.296 (Sensitivity: 0.91; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000097089
Gene: ENSMUSG00000021488
AA Change: D1103G

DomainStartEndE-ValueType
low complexity region 177 187 N/A INTRINSIC
low complexity region 281 289 N/A INTRINSIC
PWWP 322 388 1.97e-3 SMART
low complexity region 635 644 N/A INTRINSIC
low complexity region 980 1000 N/A INTRINSIC
low complexity region 1296 1309 N/A INTRINSIC
PHD 1546 1588 4.25e-8 SMART
PHD 1593 1640 3.79e-5 SMART
RING 1594 1639 1.08e-1 SMART
PHD 1641 1694 1.09e1 SMART
PHD 1710 1750 1.02e-10 SMART
PWWP 1755 1817 8.87e-29 SMART
AWS 1891 1942 3.02e-22 SMART
SET 1943 2066 1e-45 SMART
PostSET 2067 2083 3.99e-3 SMART
PHD 2121 2164 1.08e-9 SMART
low complexity region 2224 2237 N/A INTRINSIC
low complexity region 2276 2286 N/A INTRINSIC
low complexity region 2335 2356 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000224973
AA Change: D1000G

PolyPhen 2 Score 0.924 (Sensitivity: 0.81; Specificity: 0.94)
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.5%
  • 10x: 96.3%
  • 20x: 90.1%
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 containing a SET domain, 2 LXXLL motifs, 3 nuclear translocation signals (NLSs), 4 plant homeodomain (PHD) finger regions, and a proline-rich region. The encoded protein enhances androgen receptor (AR) transactivation, and this enhancement can be increased further in the presence of other androgen receptor associated coregulators. This protein may act as a nucleus-localized, basic transcriptional factor and also as a bifunctional transcriptional regulator. Mutations of this gene have been associated with Sotos syndrome and Weaver syndrome. One version of childhood acute myeloid leukemia is the result of a cryptic translocation with the breakpoints occurring within nuclear receptor-binding Su-var, enhancer of zeste, and trithorax domain protein 1 on chromosome 5 and nucleoporin, 98-kd on chromosome 11. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit excess apoptosis and retarded growth, fail to complete gastrulation, and are resorbed by embryonic day 10. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 86 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca9 T C 11: 110,042,889 (GRCm39) N387D probably benign Het
Adgrg5 T A 8: 95,660,785 (GRCm39) probably null Het
Ahi1 C A 10: 20,855,360 (GRCm39) H556Q probably damaging Het
Amph A G 13: 19,270,791 (GRCm39) probably null Het
Apol7a T C 15: 77,274,055 (GRCm39) probably benign Het
Apoo-ps A T 13: 107,550,910 (GRCm39) noncoding transcript Het
Arpc1b A G 5: 145,063,670 (GRCm39) D306G probably damaging Het
Astn2 T C 4: 65,712,795 (GRCm39) D615G probably damaging Het
Atm A G 9: 53,397,314 (GRCm39) V1673A probably damaging Het
B3gnt3 A T 8: 72,146,466 (GRCm39) V21E probably benign Het
Bco1 A G 8: 117,832,435 (GRCm39) D77G probably damaging Het
Brinp2 A T 1: 158,074,191 (GRCm39) H643Q probably damaging Het
Bsn A G 9: 107,982,941 (GRCm39) F3604S unknown Het
Cacna1c A G 6: 118,579,190 (GRCm39) F1753L probably damaging Het
Cd74 T C 18: 60,944,957 (GRCm39) S201P probably damaging Het
Cep192 T A 18: 67,940,336 (GRCm39) L101Q probably benign Het
Cfap161 T C 7: 83,442,484 (GRCm39) I110V probably null Het
Cnksr3 T C 10: 7,070,463 (GRCm39) D257G probably damaging Het
Col14a1 A C 15: 55,208,278 (GRCm39) E121A unknown Het
Cpne3 T C 4: 19,532,486 (GRCm39) D309G probably benign Het
Ctnnd1 A G 2: 84,433,240 (GRCm39) I609T probably benign Het
Cyp2s1 A G 7: 25,508,683 (GRCm39) V253A probably damaging Het
Dock7 T C 4: 98,943,586 (GRCm39) D552G possibly damaging Het
Dpyd A G 3: 119,220,924 (GRCm39) D965G probably damaging Het
Efcab2 T A 1: 178,308,911 (GRCm39) M138K probably damaging Het
Eml3 T C 19: 8,910,649 (GRCm39) S204P probably damaging Het
Fbxw16 T A 9: 109,265,236 (GRCm39) S432C possibly damaging Het
Fbxw20 T G 9: 109,061,400 (GRCm39) Q116H probably damaging Het
Fech A G 18: 64,591,240 (GRCm39) S395P probably damaging Het
Fgf7 A G 2: 125,877,875 (GRCm39) K81E probably benign Het
Fras1 T A 5: 96,929,199 (GRCm39) Y3868N possibly damaging Het
Ganab A T 19: 8,892,766 (GRCm39) probably null Het
Gfra1 T C 19: 58,288,986 (GRCm39) N153S possibly damaging Het
Gja4 T A 4: 127,205,920 (GRCm39) Y281F probably benign Het
Gm5141 T C 13: 62,921,946 (GRCm39) T407A probably damaging Het
Gm5422 T C 10: 31,125,277 (GRCm39) noncoding transcript Het
Greb1 T C 12: 16,746,457 (GRCm39) Y1271C probably damaging Het
Hp1bp3 C A 4: 137,956,080 (GRCm39) N50K possibly damaging Het
Hspg2 T C 4: 137,242,033 (GRCm39) F589S probably damaging Het
Ido1 A G 8: 25,075,260 (GRCm39) F183S probably damaging Het
Iqgap1 T A 7: 80,386,143 (GRCm39) K936I probably damaging Het
Kdm4a T C 4: 118,032,886 (GRCm39) D60G probably benign Het
L3mbtl4 G A 17: 69,081,286 (GRCm39) C558Y probably damaging Het
Lrrc28 T C 7: 67,267,833 (GRCm39) N98S probably damaging Het
Lypd11 T A 7: 24,423,622 (GRCm39) N14I possibly damaging Het
Map1a A G 2: 121,133,264 (GRCm39) D1360G probably benign Het
Megf10 C T 18: 57,410,796 (GRCm39) P702S probably benign Het
Met A G 6: 17,491,709 (GRCm39) E157G probably benign Het
Mff A G 1: 82,728,285 (GRCm39) D187G possibly damaging Het
Mlph A T 1: 90,870,630 (GRCm39) I514F possibly damaging Het
Mroh2a C T 1: 88,158,402 (GRCm39) R150* probably null Het
Myo15b T C 11: 115,755,468 (GRCm39) V976A probably benign Het
Myo9a A G 9: 59,779,209 (GRCm39) D1655G probably benign Het
Ncoa6 C T 2: 155,233,131 (GRCm39) G2059D probably benign Het
Ndst4 A T 3: 125,405,188 (GRCm39) H481L possibly damaging Het
Nipbl A G 15: 8,332,964 (GRCm39) S2220P probably benign Het
Nom1 C A 5: 29,640,309 (GRCm39) P212T probably damaging Het
Nudt9 T C 5: 104,198,467 (GRCm39) F44S possibly damaging Het
Numb C T 12: 83,842,566 (GRCm39) V537I probably damaging Het
Or10j3b T A 1: 173,043,524 (GRCm39) I102N possibly damaging Het
Or13a27 A T 7: 139,925,545 (GRCm39) M119K probably damaging Het
Or51q1c A G 7: 103,652,446 (GRCm39) probably null Het
Or5b109 A T 19: 13,211,899 (GRCm39) Y95F possibly damaging Het
Or5h17 A G 16: 58,820,063 (GRCm39) N5S probably damaging Het
Or6c211 T A 10: 129,506,248 (GRCm39) T47S probably benign Het
Osgin1 A T 8: 120,172,211 (GRCm39) Y335F probably damaging Het
Pcdh10 T A 3: 45,334,199 (GRCm39) V171E probably damaging Het
Pira13 T A 7: 3,825,762 (GRCm39) Y369F probably benign Het
Plxna4 T C 6: 32,162,436 (GRCm39) N1359S probably damaging Het
Ppp1r16a C T 15: 76,574,999 (GRCm39) probably benign Het
Prr5l T C 2: 101,602,635 (GRCm39) T2A possibly damaging Het
Rbp3 T A 14: 33,680,605 (GRCm39) I1069N possibly damaging Het
Rnf144b A G 13: 47,373,983 (GRCm39) Y60C probably damaging Het
Sbno2 A T 10: 79,903,128 (GRCm39) V396E probably damaging Het
Sdk1 A G 5: 141,940,713 (GRCm39) T494A probably benign Het
Serac1 G T 17: 6,102,031 (GRCm39) D384E probably damaging Het
Sgk1 A G 10: 21,758,556 (GRCm39) N7D probably damaging Het
Sigirr A T 7: 140,672,980 (GRCm39) V69D possibly damaging Het
Slc17a3 C T 13: 24,039,841 (GRCm39) S293F probably damaging Het
St6gal2 T C 17: 55,805,290 (GRCm39) Y396H probably benign Het
Ttn A T 2: 76,598,956 (GRCm39) F19319Y probably damaging Het
Ubr4 T A 4: 139,128,637 (GRCm39) I599N probably damaging Het
Vmn1r213 A G 13: 23,195,564 (GRCm39) probably benign Het
Vmn2r96 T A 17: 18,817,830 (GRCm39) M469K probably benign Het
Wasf1 T A 10: 40,807,902 (GRCm39) probably null Het
Wdr20rt T C 12: 65,272,689 (GRCm39) S51P probably damaging Het
Other mutations in Nsd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00777:Nsd1 APN 13 55,386,548 (GRCm39) missense probably damaging 1.00
IGL01060:Nsd1 APN 13 55,411,242 (GRCm39) missense probably damaging 1.00
IGL01125:Nsd1 APN 13 55,393,430 (GRCm39) missense probably damaging 1.00
IGL01746:Nsd1 APN 13 55,424,328 (GRCm39) splice site probably null
IGL02437:Nsd1 APN 13 55,461,254 (GRCm39) missense probably damaging 1.00
IGL02530:Nsd1 APN 13 55,450,646 (GRCm39) splice site probably benign
IGL02557:Nsd1 APN 13 55,460,261 (GRCm39) missense probably damaging 1.00
IGL02572:Nsd1 APN 13 55,443,943 (GRCm39) missense probably damaging 1.00
IGL02665:Nsd1 APN 13 55,443,996 (GRCm39) missense probably damaging 1.00
IGL02870:Nsd1 APN 13 55,461,416 (GRCm39) missense probably benign 0.06
IGL03181:Nsd1 APN 13 55,394,858 (GRCm39) missense probably damaging 1.00
Amanuensis UTSW 13 55,409,439 (GRCm39) nonsense probably null
handwriting UTSW 13 55,461,359 (GRCm39) missense
Prothonotary UTSW 13 55,430,570 (GRCm39) missense probably damaging 1.00
scribe UTSW 13 55,439,049 (GRCm39) missense probably damaging 1.00
stenographer UTSW 13 55,446,189 (GRCm39) splice site probably null
PIT4480001:Nsd1 UTSW 13 55,361,731 (GRCm39) missense probably benign 0.11
R0316:Nsd1 UTSW 13 55,361,584 (GRCm39) missense probably damaging 0.98
R0519:Nsd1 UTSW 13 55,460,648 (GRCm39) missense probably benign 0.04
R0542:Nsd1 UTSW 13 55,408,271 (GRCm39) missense possibly damaging 0.93
R0563:Nsd1 UTSW 13 55,394,391 (GRCm39) missense possibly damaging 0.48
R0906:Nsd1 UTSW 13 55,425,403 (GRCm39) missense probably benign 0.30
R1560:Nsd1 UTSW 13 55,394,533 (GRCm39) nonsense probably null
R1572:Nsd1 UTSW 13 55,394,782 (GRCm39) missense probably damaging 0.98
R1693:Nsd1 UTSW 13 55,395,074 (GRCm39) missense probably benign
R1697:Nsd1 UTSW 13 55,361,872 (GRCm39) critical splice acceptor site probably null
R1720:Nsd1 UTSW 13 55,394,711 (GRCm39) missense probably damaging 0.98
R1829:Nsd1 UTSW 13 55,394,182 (GRCm39) missense probably damaging 1.00
R1834:Nsd1 UTSW 13 55,461,164 (GRCm39) missense possibly damaging 0.52
R1842:Nsd1 UTSW 13 55,394,258 (GRCm39) missense probably damaging 1.00
R1880:Nsd1 UTSW 13 55,361,606 (GRCm39) missense probably damaging 0.99
R2022:Nsd1 UTSW 13 55,361,092 (GRCm39) missense probably damaging 0.99
R2075:Nsd1 UTSW 13 55,458,313 (GRCm39) missense possibly damaging 0.74
R2143:Nsd1 UTSW 13 55,408,210 (GRCm39) missense probably damaging 1.00
R2151:Nsd1 UTSW 13 55,439,049 (GRCm39) missense probably damaging 1.00
R2316:Nsd1 UTSW 13 55,381,779 (GRCm39) missense probably damaging 1.00
R2359:Nsd1 UTSW 13 55,361,524 (GRCm39) missense possibly damaging 0.90
R2361:Nsd1 UTSW 13 55,361,524 (GRCm39) missense possibly damaging 0.90
R2656:Nsd1 UTSW 13 55,394,681 (GRCm39) missense probably damaging 1.00
R2849:Nsd1 UTSW 13 55,361,505 (GRCm39) missense probably damaging 0.99
R3237:Nsd1 UTSW 13 55,460,701 (GRCm39) missense possibly damaging 0.92
R3772:Nsd1 UTSW 13 55,394,486 (GRCm39) missense probably benign 0.00
R3773:Nsd1 UTSW 13 55,394,486 (GRCm39) missense probably benign 0.00
R3849:Nsd1 UTSW 13 55,394,504 (GRCm39) missense probably benign 0.00
R3951:Nsd1 UTSW 13 55,416,267 (GRCm39) missense probably benign 0.05
R4036:Nsd1 UTSW 13 55,361,524 (GRCm39) missense possibly damaging 0.90
R4073:Nsd1 UTSW 13 55,395,541 (GRCm39) missense probably benign 0.28
R4080:Nsd1 UTSW 13 55,449,622 (GRCm39) missense probably damaging 0.96
R4226:Nsd1 UTSW 13 55,408,214 (GRCm39) missense probably damaging 1.00
R4485:Nsd1 UTSW 13 55,393,434 (GRCm39) missense probably benign
R4703:Nsd1 UTSW 13 55,361,876 (GRCm39) missense probably damaging 1.00
R4853:Nsd1 UTSW 13 55,416,317 (GRCm39) missense probably benign 0.30
R4915:Nsd1 UTSW 13 55,424,341 (GRCm39) missense probably benign 0.00
R4915:Nsd1 UTSW 13 55,395,681 (GRCm39) missense possibly damaging 0.65
R5264:Nsd1 UTSW 13 55,395,159 (GRCm39) missense possibly damaging 0.49
R5348:Nsd1 UTSW 13 55,460,147 (GRCm39) missense probably benign 0.00
R5473:Nsd1 UTSW 13 55,395,585 (GRCm39) missense probably damaging 1.00
R5498:Nsd1 UTSW 13 55,361,115 (GRCm39) nonsense probably null
R5503:Nsd1 UTSW 13 55,393,752 (GRCm39) missense probably damaging 1.00
R5511:Nsd1 UTSW 13 55,460,543 (GRCm39) missense probably benign 0.00
R5683:Nsd1 UTSW 13 55,393,961 (GRCm39) missense probably benign 0.00
R5778:Nsd1 UTSW 13 55,454,792 (GRCm39) missense probably damaging 1.00
R5793:Nsd1 UTSW 13 55,395,819 (GRCm39) missense probably benign
R5922:Nsd1 UTSW 13 55,395,288 (GRCm39) missense probably benign 0.01
R5956:Nsd1 UTSW 13 55,411,217 (GRCm39) missense probably damaging 1.00
R6053:Nsd1 UTSW 13 55,441,422 (GRCm39) missense probably damaging 1.00
R6141:Nsd1 UTSW 13 55,439,097 (GRCm39) missense probably damaging 1.00
R6158:Nsd1 UTSW 13 55,393,434 (GRCm39) missense probably benign
R6224:Nsd1 UTSW 13 55,460,945 (GRCm39) missense possibly damaging 0.85
R6396:Nsd1 UTSW 13 55,386,602 (GRCm39) missense probably damaging 1.00
R6598:Nsd1 UTSW 13 55,441,515 (GRCm39) missense possibly damaging 0.94
R7170:Nsd1 UTSW 13 55,409,439 (GRCm39) nonsense probably null
R7205:Nsd1 UTSW 13 55,394,283 (GRCm39) missense probably damaging 1.00
R7215:Nsd1 UTSW 13 55,395,454 (GRCm39) missense probably benign 0.00
R7337:Nsd1 UTSW 13 55,394,022 (GRCm39) missense probably damaging 1.00
R7432:Nsd1 UTSW 13 55,361,187 (GRCm39) missense probably benign
R7638:Nsd1 UTSW 13 55,460,141 (GRCm39) missense probably benign 0.01
R7647:Nsd1 UTSW 13 55,447,648 (GRCm39) missense probably damaging 0.96
R7658:Nsd1 UTSW 13 55,425,452 (GRCm39) missense probably damaging 1.00
R7884:Nsd1 UTSW 13 55,461,068 (GRCm39) missense probably damaging 0.99
R8032:Nsd1 UTSW 13 55,458,196 (GRCm39) missense probably damaging 1.00
R8113:Nsd1 UTSW 13 55,393,434 (GRCm39) missense probably benign
R8152:Nsd1 UTSW 13 55,458,180 (GRCm39) missense possibly damaging 0.49
R8183:Nsd1 UTSW 13 55,460,186 (GRCm39) missense probably damaging 1.00
R8432:Nsd1 UTSW 13 55,395,516 (GRCm39) missense possibly damaging 0.91
R8462:Nsd1 UTSW 13 55,446,189 (GRCm39) splice site probably null
R8469:Nsd1 UTSW 13 55,425,366 (GRCm39) missense possibly damaging 0.76
R8756:Nsd1 UTSW 13 55,461,506 (GRCm39) missense probably benign 0.00
R8867:Nsd1 UTSW 13 55,430,570 (GRCm39) missense probably damaging 1.00
R9035:Nsd1 UTSW 13 55,393,667 (GRCm39) missense possibly damaging 0.79
R9101:Nsd1 UTSW 13 55,461,359 (GRCm39) missense
R9154:Nsd1 UTSW 13 55,361,253 (GRCm39) missense probably damaging 1.00
R9155:Nsd1 UTSW 13 55,361,253 (GRCm39) missense probably damaging 1.00
R9262:Nsd1 UTSW 13 55,394,871 (GRCm39) missense possibly damaging 0.92
R9592:Nsd1 UTSW 13 55,424,355 (GRCm39) missense probably damaging 1.00
R9604:Nsd1 UTSW 13 55,381,807 (GRCm39) missense probably benign 0.25
R9712:Nsd1 UTSW 13 55,393,856 (GRCm39) missense possibly damaging 0.81
R9716:Nsd1 UTSW 13 55,458,313 (GRCm39) missense possibly damaging 0.74
R9787:Nsd1 UTSW 13 55,461,518 (GRCm39) missense probably benign 0.15
Z1088:Nsd1 UTSW 13 55,361,661 (GRCm39) missense possibly damaging 0.83
Z1176:Nsd1 UTSW 13 55,393,338 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACTGTATCCCAAGGCGCAACTG -3'
(R):5'- TCCAAAAGCACCCTCCGAGTTTTC -3'

Sequencing Primer
(F):5'- GTTGAGAGAAACCATTTCAGCC -3'
(R):5'- GGTTTAATCGCTGCCACCG -3'
Posted On 2013-07-30