Incidental Mutation 'R1533:Ncdn'
ID 166728
Institutional Source Beutler Lab
Gene Symbol Ncdn
Ensembl Gene ENSMUSG00000028833
Gene Name neurochondrin
Synonyms neurochondrin-2, neurochondrin-1, norbin
MMRRC Submission 039572-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1533 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 126637543-126647231 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) C to A at 126642491 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Stop codon at position 389 (E389*)
Ref Sequence ENSEMBL: ENSMUSP00000101722 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030637] [ENSMUST00000102608] [ENSMUST00000106116] [ENSMUST00000148935] [ENSMUST00000154640]
AlphaFold Q9Z0E0
Predicted Effect probably null
Transcript: ENSMUST00000030637
AA Change: E389*
SMART Domains Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: E389*

DomainStartEndE-ValueType
Pfam:Neurochondrin 30 637 3e-209 PFAM
low complexity region 649 659 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000102608
SMART Domains Protein: ENSMUSP00000099668
Gene: ENSMUSG00000028830

DomainStartEndE-ValueType
low complexity region 83 97 N/A INTRINSIC
FN3 113 391 8.45e1 SMART
IG_like 305 398 3.57e1 SMART
PKD 309 400 3.1e-1 SMART
FN3 399 485 2.7e1 SMART
PKD 408 497 1.87e-4 SMART
FN3 502 676 4.47e1 SMART
PKD 503 593 3.22e-8 SMART
IG_like 508 591 1.17e1 SMART
IG_like 597 782 1.66e2 SMART
PKD 599 687 8.98e-7 SMART
PKD 693 784 1.05e-7 SMART
FN3 694 772 3.71e1 SMART
transmembrane domain 927 949 N/A INTRINSIC
low complexity region 995 1010 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000106116
AA Change: E389*
SMART Domains Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: E389*

DomainStartEndE-ValueType
Pfam:Neurochondrin 30 637 9.1e-217 PFAM
low complexity region 649 659 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127079
Predicted Effect probably benign
Transcript: ENSMUST00000148935
Predicted Effect probably benign
Transcript: ENSMUST00000154640
SMART Domains Protein: ENSMUSP00000122352
Gene: ENSMUSG00000028830

DomainStartEndE-ValueType
low complexity region 83 97 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.4%
  • 20x: 92.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a leucine-rich cytoplasmic protein, which is highly similar to a mouse protein that negatively regulates Ca/calmodulin-dependent protein kinase II phosphorylation and may be essential for spatial learning processes. Several alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jul 2008]
PHENOTYPE: Targeted inactivation of this gene results in early embryonic lethality in the homozygous state and impaired chondrocyte proliferation and differentiation in the heterozygous state. Gene trap mutation resulted in lacrimal gland hypertrophy. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca4 G C 3: 121,928,807 (GRCm39) G1340A probably benign Het
Ambra1 T A 2: 91,717,210 (GRCm39) Y836N probably damaging Het
Arhgap26 A T 18: 39,504,130 (GRCm39) H144L probably benign Het
B3gnt5 A G 16: 19,588,364 (GRCm39) I194M probably damaging Het
Bltp1 G T 3: 37,095,524 (GRCm39) G4509V probably damaging Het
Bod1l A T 5: 41,979,498 (GRCm39) C605* probably null Het
C2cd3 G T 7: 100,055,284 (GRCm39) K482N possibly damaging Het
Cd300lg T A 11: 101,934,047 (GRCm39) L98Q probably damaging Het
Cerkl T A 2: 79,171,701 (GRCm39) I386F possibly damaging Het
Cfh T A 1: 140,028,716 (GRCm39) D466V possibly damaging Het
Crtc1 A T 8: 70,850,949 (GRCm39) I221N probably damaging Het
Ctnnbl1 T C 2: 157,678,563 (GRCm39) S389P probably benign Het
Ctsb A T 14: 63,376,544 (GRCm39) D258V probably damaging Het
Cuzd1 G T 7: 130,913,432 (GRCm39) T395N probably damaging Het
Dnah6 T C 6: 73,128,536 (GRCm39) T1240A probably benign Het
Dok7 T A 5: 35,221,671 (GRCm39) probably null Het
Dscaml1 T C 9: 45,361,882 (GRCm39) V214A probably damaging Het
Enpp6 A T 8: 47,518,469 (GRCm39) Y199F probably benign Het
Entpd5 C A 12: 84,441,434 (GRCm39) K111N probably damaging Het
Fam98a A G 17: 75,848,276 (GRCm39) L146S probably damaging Het
Fhod3 A T 18: 25,248,921 (GRCm39) I1367F probably damaging Het
Fmnl2 A G 2: 52,995,549 (GRCm39) E424G probably damaging Het
Fpr3 T A 17: 18,190,922 (GRCm39) Y64* probably null Het
Fzd6 A T 15: 38,895,019 (GRCm39) H395L probably damaging Het
Gcsh T A 8: 117,715,921 (GRCm39) H54L probably damaging Het
Gsdma T A 11: 98,567,210 (GRCm39) S437T unknown Het
Gzmc A G 14: 56,471,376 (GRCm39) V55A probably damaging Het
Hecw2 T A 1: 53,965,704 (GRCm39) probably null Het
Ifi207 A G 1: 173,555,306 (GRCm39) V792A probably benign Het
Itpr3 C A 17: 27,314,534 (GRCm39) N661K possibly damaging Het
Jmy A T 13: 93,577,819 (GRCm39) I783N probably benign Het
Kcmf1 T C 6: 72,820,003 (GRCm39) E281G possibly damaging Het
Klra3 G C 6: 130,310,107 (GRCm39) R138G probably benign Het
Lgr6 T A 1: 135,032,670 (GRCm39) Y70F possibly damaging Het
Lnx1 T G 5: 74,780,678 (GRCm39) D330A probably damaging Het
Lrp5 T C 19: 3,664,234 (GRCm39) N106S probably benign Het
Mamdc4 C A 2: 25,459,759 (GRCm39) R135L possibly damaging Het
Mcm3ap A G 10: 76,340,121 (GRCm39) E1464G probably damaging Het
Megf8 T C 7: 25,034,280 (GRCm39) V666A possibly damaging Het
Mettl3 T A 14: 52,534,385 (GRCm39) E331D probably benign Het
Mphosph9 T C 5: 124,405,204 (GRCm39) K789R probably damaging Het
Mtf2 T C 5: 108,239,995 (GRCm39) L234P probably damaging Het
Ndor1 A G 2: 25,139,279 (GRCm39) S231P probably damaging Het
Nelfa T G 5: 34,056,215 (GRCm39) K483Q probably damaging Het
Odad1 T A 7: 45,592,282 (GRCm39) M354K probably benign Het
Opn1sw C T 6: 29,378,923 (GRCm39) R243Q probably benign Het
Or13a24 T A 7: 140,155,034 (GRCm39) probably null Het
Or9e1 A G 11: 58,732,792 (GRCm39) N284S probably damaging Het
Pik3cd T C 4: 149,739,653 (GRCm39) E584G probably damaging Het
Plcb3 A T 19: 6,935,041 (GRCm39) M870K possibly damaging Het
Poc5 A G 13: 96,528,152 (GRCm39) D16G probably damaging Het
Prpf40a A G 2: 53,035,852 (GRCm39) I633T probably damaging Het
Ptpn13 G T 5: 103,704,044 (GRCm39) E1359* probably null Het
Ptprr C A 10: 116,024,113 (GRCm39) Y4* probably null Het
Rbm45 T C 2: 76,202,503 (GRCm39) probably null Het
Rfng C T 11: 120,672,687 (GRCm39) W320* probably null Het
Rgs6 G T 12: 83,138,547 (GRCm39) V294L probably benign Het
Rufy4 T C 1: 74,169,002 (GRCm39) probably null Het
Ruvbl2 T A 7: 45,073,566 (GRCm39) N313I probably damaging Het
Sema4g G A 19: 44,981,256 (GRCm39) V70M probably damaging Het
Siglec1 T C 2: 130,918,078 (GRCm39) T969A probably benign Het
Slc22a27 T A 19: 7,844,348 (GRCm39) T431S possibly damaging Het
Slc25a16 G A 10: 62,756,643 (GRCm39) R38H probably damaging Het
Slc38a6 T C 12: 73,391,626 (GRCm39) V296A probably benign Het
Slc39a11 C T 11: 113,196,748 (GRCm39) V212I probably damaging Het
Sltm A G 9: 70,493,948 (GRCm39) K782E probably damaging Het
Styxl1 T A 5: 135,799,175 (GRCm39) Y23F probably damaging Het
Svs4 T C 2: 164,120,148 (GRCm39) I20V unknown Het
Syt14 G T 1: 192,613,084 (GRCm39) T572K possibly damaging Het
Tbc1d5 A T 17: 51,227,603 (GRCm39) I214N possibly damaging Het
Tm9sf3 A G 19: 41,227,223 (GRCm39) S283P probably benign Het
Tmtc1 C T 6: 148,147,208 (GRCm39) probably null Het
Ttll7 T A 3: 146,602,422 (GRCm39) N73K probably damaging Het
Ttn T A 2: 76,602,802 (GRCm39) K18473N probably damaging Het
Ubr2 A C 17: 47,278,173 (GRCm39) Y721* probably null Het
Vmn1r14 T A 6: 57,211,286 (GRCm39) I288N probably damaging Het
Vmn2r103 T C 17: 19,993,662 (GRCm39) I13T probably benign Het
Vps13a A T 19: 16,678,494 (GRCm39) Y1162* probably null Het
Vps51 C A 19: 6,121,497 (GRCm39) R175L probably benign Het
Zfp523 C A 17: 28,423,473 (GRCm39) S149R probably benign Het
Zik1 A G 7: 10,224,053 (GRCm39) I348T possibly damaging Het
Znfx1 T A 2: 166,898,708 (GRCm39) H72L probably benign Het
Other mutations in Ncdn
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00340:Ncdn APN 4 126,640,981 (GRCm39) missense probably benign 0.00
R0031:Ncdn UTSW 4 126,643,901 (GRCm39) splice site probably null
R0135:Ncdn UTSW 4 126,640,462 (GRCm39) missense probably benign 0.37
R0413:Ncdn UTSW 4 126,644,327 (GRCm39) missense possibly damaging 0.52
R1404:Ncdn UTSW 4 126,643,833 (GRCm39) missense probably benign 0.33
R1404:Ncdn UTSW 4 126,643,833 (GRCm39) missense probably benign 0.33
R1486:Ncdn UTSW 4 126,642,391 (GRCm39) missense probably damaging 1.00
R1785:Ncdn UTSW 4 126,639,066 (GRCm39) critical splice acceptor site probably null
R1786:Ncdn UTSW 4 126,639,066 (GRCm39) critical splice acceptor site probably null
R1789:Ncdn UTSW 4 126,645,796 (GRCm39) missense probably damaging 1.00
R1791:Ncdn UTSW 4 126,645,732 (GRCm39) critical splice donor site probably null
R3406:Ncdn UTSW 4 126,642,388 (GRCm39) missense probably benign 0.09
R4547:Ncdn UTSW 4 126,640,467 (GRCm39) missense probably damaging 1.00
R4863:Ncdn UTSW 4 126,644,216 (GRCm39) missense probably damaging 1.00
R4916:Ncdn UTSW 4 126,643,731 (GRCm39) missense possibly damaging 0.89
R4917:Ncdn UTSW 4 126,643,731 (GRCm39) missense possibly damaging 0.89
R4918:Ncdn UTSW 4 126,643,731 (GRCm39) missense possibly damaging 0.89
R5218:Ncdn UTSW 4 126,644,603 (GRCm39) missense probably benign 0.13
R5356:Ncdn UTSW 4 126,641,021 (GRCm39) missense probably damaging 1.00
R5617:Ncdn UTSW 4 126,638,840 (GRCm39) missense probably damaging 0.99
R5718:Ncdn UTSW 4 126,643,743 (GRCm39) nonsense probably null
R6057:Ncdn UTSW 4 126,638,824 (GRCm39) missense probably benign 0.05
R6343:Ncdn UTSW 4 126,640,964 (GRCm39) missense possibly damaging 0.74
R6986:Ncdn UTSW 4 126,641,022 (GRCm39) missense probably damaging 1.00
R6988:Ncdn UTSW 4 126,640,982 (GRCm39) missense probably benign 0.00
R8257:Ncdn UTSW 4 126,643,676 (GRCm39) critical splice donor site probably null
R8279:Ncdn UTSW 4 126,644,199 (GRCm39) missense probably benign 0.00
R8804:Ncdn UTSW 4 126,643,898 (GRCm39) missense probably benign 0.09
R8812:Ncdn UTSW 4 126,638,905 (GRCm39) missense possibly damaging 0.52
R9047:Ncdn UTSW 4 126,644,621 (GRCm39) missense possibly damaging 0.69
R9206:Ncdn UTSW 4 126,644,041 (GRCm39) missense probably benign 0.03
R9208:Ncdn UTSW 4 126,644,041 (GRCm39) missense probably benign 0.03
R9289:Ncdn UTSW 4 126,643,903 (GRCm39) missense possibly damaging 0.81
R9353:Ncdn UTSW 4 126,644,464 (GRCm39) missense probably benign 0.00
R9420:Ncdn UTSW 4 126,645,762 (GRCm39) missense probably damaging 1.00
R9578:Ncdn UTSW 4 126,645,795 (GRCm39) missense probably damaging 1.00
R9687:Ncdn UTSW 4 126,642,467 (GRCm39) missense probably damaging 1.00
R9698:Ncdn UTSW 4 126,643,688 (GRCm39) missense probably damaging 1.00
R9778:Ncdn UTSW 4 126,642,467 (GRCm39) missense probably damaging 1.00
R9781:Ncdn UTSW 4 126,642,467 (GRCm39) missense probably damaging 1.00
Z1176:Ncdn UTSW 4 126,643,946 (GRCm39) missense probably benign 0.05
Z1176:Ncdn UTSW 4 126,643,944 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACCTGCTGCGAAATGTCACTGG -3'
(R):5'- GATTCCATTGTCCACACTGAGGTCC -3'

Sequencing Primer
(F):5'- CGAAATGTCACTGGCCTCC -3'
(R):5'- gtctctcccttcacgctg -3'
Posted On 2014-04-13