Incidental Mutation 'R1791:Ncdn'
ID 201705
Institutional Source Beutler Lab
Gene Symbol Ncdn
Ensembl Gene ENSMUSG00000028833
Gene Name neurochondrin
Synonyms neurochondrin-2, neurochondrin-1, norbin
MMRRC Submission 039821-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1791 (G1)
Quality Score 92
Status Validated
Chromosome 4
Chromosomal Location 126637543-126647231 bp(-) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) A to G at 126645732 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000101722 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030637] [ENSMUST00000047431] [ENSMUST00000102607] [ENSMUST00000102608] [ENSMUST00000106116] [ENSMUST00000132660] [ENSMUST00000148935] [ENSMUST00000154640]
AlphaFold Q9Z0E0
Predicted Effect probably null
Transcript: ENSMUST00000030637
SMART Domains Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833

DomainStartEndE-ValueType
Pfam:Neurochondrin 30 637 3e-209 PFAM
low complexity region 649 659 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000047431
SMART Domains Protein: ENSMUSP00000037802
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 benign
Transcript: ENSMUST00000102607
SMART Domains Protein: ENSMUSP00000099667
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 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
SMART Domains Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833

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 noncoding transcript
Transcript: ENSMUST00000136035
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131900
Predicted Effect probably benign
Transcript: ENSMUST00000132660
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
Meta Mutation Damage Score 0.9488 question?
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.0%
  • 20x: 91.6%
Validation Efficiency 95% (104/110)
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: 104 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m C A 6: 121,631,571 (GRCm39) L623M probably benign Het
Adrm1b T A 3: 92,335,538 (GRCm39) D388V probably damaging Het
Akap13 T G 7: 75,260,783 (GRCm39) C333G probably benign Het
Akap6 T C 12: 53,115,908 (GRCm39) S1004P probably damaging Het
Akap7 T C 10: 25,115,583 (GRCm39) T181A probably benign Het
Ap3b1 A G 13: 94,545,305 (GRCm39) E186G possibly damaging Het
Arhgap17 T C 7: 122,885,925 (GRCm39) T736A probably benign Het
Bltp3a T A 17: 28,113,720 (GRCm39) D1297E probably damaging Het
Bmp8a G T 4: 123,218,378 (GRCm39) R214S possibly damaging Het
Cacna1f T C X: 7,486,678 (GRCm39) S890P probably damaging Het
Cd96 A T 16: 45,938,362 (GRCm39) Y34* probably null Het
Cdc42ep4 A G 11: 113,620,163 (GRCm39) L76P probably damaging Het
Cdh23 A G 10: 60,227,505 (GRCm39) V1195A possibly damaging Het
Cfap57 G A 4: 118,428,921 (GRCm39) T1015M possibly damaging Het
Chrm3 C A 13: 9,927,452 (GRCm39) G528V probably damaging Het
Cimap1c A T 9: 56,759,027 (GRCm39) F43I possibly damaging Het
Clip4 T C 17: 72,108,937 (GRCm39) probably benign Het
Col9a1 A T 1: 24,224,386 (GRCm39) R189S unknown Het
Cul4b A T X: 37,636,728 (GRCm39) I481N probably damaging Het
Cyp26b1 A G 6: 84,561,441 (GRCm39) S74P probably benign Het
Cyp3a57 A G 5: 145,307,820 (GRCm39) N192S probably benign Het
Dcbld1 A G 10: 52,195,572 (GRCm39) D260G probably damaging Het
Dhrs7 T C 12: 72,699,939 (GRCm39) N231S probably benign Het
Disp3 G A 4: 148,325,975 (GRCm39) P1261L probably damaging Het
Dnaaf4 T C 9: 72,867,966 (GRCm39) Y76H possibly damaging Het
Eml5 C A 12: 98,853,315 (GRCm39) V95F probably benign Het
Emsy A G 7: 98,297,087 (GRCm39) I32T probably damaging Het
Esr1 A G 10: 4,733,913 (GRCm39) R238G probably damaging Het
Exosc1 T C 19: 41,916,524 (GRCm39) K84R probably benign Het
F830016B08Rik T A 18: 60,433,589 (GRCm39) V224E probably benign Het
Fam228a T A 12: 4,782,748 (GRCm39) N115I probably damaging Het
Farp1 T C 14: 121,494,157 (GRCm39) I546T probably damaging Het
Fbxo30 T A 10: 11,165,531 (GRCm39) C84* probably null Het
Fbxw17 A G 13: 50,579,810 (GRCm39) probably benign Het
Foxo4 G C X: 100,302,069 (GRCm39) R192P probably benign Het
Galnt7 G T 8: 57,995,564 (GRCm39) T377K probably benign Het
Garnl3 T C 2: 32,924,139 (GRCm39) I248V probably benign Het
Glod4 A G 11: 76,128,534 (GRCm39) Y104H probably damaging Het
Glrb T C 3: 80,767,482 (GRCm39) Y246C probably damaging Het
Gm5292 A G 5: 44,101,752 (GRCm39) noncoding transcript Het
Gm5424 C A 10: 61,908,086 (GRCm39) noncoding transcript Het
Gm7276 C T 18: 77,273,431 (GRCm39) probably benign Het
Golga5 A G 12: 102,458,390 (GRCm39) N611S possibly damaging Het
Gucy2c A C 6: 136,721,025 (GRCm39) Y391D probably damaging Het
H6pd A G 4: 150,066,130 (GRCm39) I760T probably damaging Het
Hapln2 T A 3: 87,931,712 (GRCm39) I5F possibly damaging Het
Hdac11 G T 6: 91,145,806 (GRCm39) V169L probably benign Het
Hectd2 T C 19: 36,586,816 (GRCm39) V557A possibly damaging Het
Huwe1 T A X: 150,647,749 (GRCm39) N747K probably benign Het
Ints1 A G 5: 139,760,277 (GRCm39) S66P probably benign Het
Ipo7 A G 7: 109,626,339 (GRCm39) D49G probably damaging Het
Itgb4 G A 11: 115,879,346 (GRCm39) C575Y probably damaging Het
Klhl3 A G 13: 58,181,044 (GRCm39) V250A possibly damaging Het
Klk1b24 A G 7: 43,839,852 (GRCm39) probably null Het
Map3k11 T A 19: 5,745,600 (GRCm39) Y333* probably null Het
Mbp A G 18: 82,572,474 (GRCm39) T57A probably benign Het
Myh9 A G 15: 77,657,464 (GRCm39) probably benign Het
Mypn C T 10: 62,961,472 (GRCm39) R1040Q probably damaging Het
Ndn C T 7: 61,998,256 (GRCm39) P34L probably benign Het
Or10ab5 T A 7: 108,245,571 (GRCm39) T71S probably benign Het
Or11h4 AGGGATTGGG AGGGATTGGGATTGGG 14: 50,974,144 (GRCm39) probably benign Het
Or4k15c A G 14: 50,321,499 (GRCm39) F213S probably benign Het
Or51b6b T C 7: 103,310,005 (GRCm39) probably null Het
Or51f1 G A 7: 102,505,569 (GRCm39) Q307* probably null Het
Or8d2 T A 9: 38,759,901 (GRCm39) S164T possibly damaging Het
Pbx3 T C 2: 34,114,464 (GRCm39) T82A possibly damaging Het
Pi15 T C 1: 17,672,945 (GRCm39) F48S probably benign Het
Pkhd1 A G 1: 20,655,376 (GRCm39) probably benign Het
Ppard C G 17: 28,505,348 (GRCm39) R12G unknown Het
Prrc2c G T 1: 162,532,551 (GRCm39) probably benign Het
Prune1 A G 3: 95,175,553 (GRCm39) Y41H possibly damaging Het
Rcsd1 T C 1: 165,483,541 (GRCm39) D150G probably damaging Het
Rgs12 A T 5: 35,123,456 (GRCm39) Q413L possibly damaging Het
Rhox2h A G X: 36,850,848 (GRCm39) Y185H probably damaging Het
Rnf17 T A 14: 56,741,464 (GRCm39) C1306* probably null Het
Ros1 T A 10: 51,976,183 (GRCm39) M1499L probably benign Het
Rubcnl T C 14: 75,284,989 (GRCm39) S503P probably damaging Het
Sap18b A T 8: 96,552,342 (GRCm39) R117S probably benign Het
Shank2 A G 7: 143,964,336 (GRCm39) E858G probably damaging Het
Shtn1 T C 19: 59,020,632 (GRCm39) R197G probably damaging Het
Slamf8 G A 1: 172,412,087 (GRCm39) R163* probably null Het
Slc6a3 T C 13: 73,714,411 (GRCm39) I392T possibly damaging Het
Sp140 C T 1: 85,547,772 (GRCm39) probably benign Het
Sp8 T C 12: 118,812,751 (GRCm39) V202A possibly damaging Het
Spata13 T C 14: 60,946,908 (GRCm39) V652A probably damaging Het
Stpg2 A T 3: 139,023,162 (GRCm39) T393S probably benign Het
Tagap T C 17: 8,150,299 (GRCm39) M228T probably damaging Het
Tagap A G 17: 8,152,377 (GRCm39) T521A probably benign Het
Tas2r123 T G 6: 132,824,528 (GRCm39) S142A probably damaging Het
Tat T A 8: 110,718,261 (GRCm39) S49T probably benign Het
Tfap4 G T 16: 4,369,933 (GRCm39) Q41K possibly damaging Het
Thbs2 T C 17: 14,906,075 (GRCm39) N275S probably benign Het
Tnfsf14 T A 17: 57,497,867 (GRCm39) R122W probably damaging Het
Tnrc6a T C 7: 122,792,140 (GRCm39) V1886A possibly damaging Het
Trim56 G A 5: 137,143,252 (GRCm39) A88V probably damaging Het
Trio A G 15: 27,841,842 (GRCm39) Y1081H probably damaging Het
Tspear T A 10: 77,706,253 (GRCm39) L341H possibly damaging Het
Ube2o G A 11: 116,432,320 (GRCm39) T882I probably benign Het
Upk3a A G 15: 84,904,815 (GRCm39) T188A possibly damaging Het
Vmn1r79 A C 7: 11,910,358 (GRCm39) D80A probably damaging Het
Wls C A 3: 159,617,450 (GRCm39) T375K probably benign Het
Wnt5a T C 14: 28,233,835 (GRCm39) M1T probably null Het
Zcchc4 A G 5: 52,953,932 (GRCm39) E204G probably damaging Het
Zfp513 G A 5: 31,357,678 (GRCm39) P232S possibly damaging 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
R1533:Ncdn UTSW 4 126,642,491 (GRCm39) nonsense probably null
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
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'- ATGAGTCAGCTCCCATCTGC -3'
(R):5'- GATGCTCAGTCCCTCTTGTG -3'

Sequencing Primer
(F):5'- TGGTCCCATGCCACAGTC -3'
(R):5'- GTTCACAGTTGGGCAAGGC -3'
Posted On 2014-06-23