Incidental Mutation 'R5617:Ncdn'
ID 439572
Institutional Source Beutler Lab
Gene Symbol Ncdn
Ensembl Gene ENSMUSG00000028833
Gene Name neurochondrin
Synonyms neurochondrin-2, neurochondrin-1, norbin
MMRRC Submission 043276-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5617 (G1)
Quality Score 170
Status Validated
Chromosome 4
Chromosomal Location 126637543-126647231 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 126638840 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Cysteine at position 660 (R660C)
Ref Sequence ENSEMBL: ENSMUSP00000101722 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030637] [ENSMUST00000106116]
AlphaFold Q9Z0E0
Predicted Effect probably damaging
Transcript: ENSMUST00000030637
AA Change: R660C

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: R660C

DomainStartEndE-ValueType
Pfam:Neurochondrin 30 637 3e-209 PFAM
low complexity region 649 659 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000106116
AA Change: R660C

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: R660C

DomainStartEndE-ValueType
Pfam:Neurochondrin 30 637 9.1e-217 PFAM
low complexity region 649 659 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127079
Meta Mutation Damage Score 0.3195 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.6%
Validation Efficiency 100% (59/59)
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 C T 11: 9,227,891 (GRCm39) L645F probably benign Het
Acss3 T C 10: 106,787,851 (GRCm39) Y522C probably damaging Het
Asb18 A G 1: 89,882,184 (GRCm39) V118A possibly damaging Het
Aste1 T A 9: 105,275,034 (GRCm39) C8S probably benign Het
Atp10a A G 7: 58,453,423 (GRCm39) S834G probably benign Het
Cdh18 A G 15: 23,226,854 (GRCm39) D105G probably damaging Het
Cenpb T C 2: 131,020,934 (GRCm39) E288G probably damaging Het
Clcnka C T 4: 141,116,628 (GRCm39) G541D probably null Het
Dctn3 T C 4: 41,716,407 (GRCm39) I134V possibly damaging Het
Dennd4b T C 3: 90,182,933 (GRCm39) S917P probably benign Het
Fam135b A T 15: 71,493,865 (GRCm39) D21E probably damaging Het
Fam174a T C 1: 95,241,972 (GRCm39) V144A probably damaging Het
Fbxo38 A G 18: 62,639,042 (GRCm39) Y1087H probably damaging Het
Gm7275 A T 16: 47,894,527 (GRCm39) noncoding transcript Het
Gm9271 G T 7: 39,013,076 (GRCm39) noncoding transcript Het
Grm2 T C 9: 106,528,275 (GRCm39) probably null Het
Htt T A 5: 35,028,150 (GRCm39) V1802D possibly damaging Het
Ighv1-75 C A 12: 115,797,874 (GRCm39) G16V probably benign Het
Krt78 G A 15: 101,856,044 (GRCm39) T589I probably damaging Het
Lama3 T C 18: 12,631,993 (GRCm39) probably benign Het
Lbr A T 1: 181,656,467 (GRCm39) V227D probably benign Het
Lsamp T C 16: 41,954,786 (GRCm39) V211A probably damaging Het
Map3k19 G A 1: 127,750,703 (GRCm39) R883C probably damaging Het
Marchf8 A C 6: 116,380,481 (GRCm39) I111L possibly damaging Het
Mrps10 T A 17: 47,689,167 (GRCm39) M187K probably benign Het
Notum A T 11: 120,547,171 (GRCm39) Y332* probably null Het
Nr1h5 A T 3: 102,855,145 (GRCm39) L319I probably damaging Het
Or51q1 A T 7: 103,628,921 (GRCm39) H180L possibly damaging Het
Or8k35 T A 2: 86,424,345 (GRCm39) I276L probably benign Het
Osbpl5 T C 7: 143,246,684 (GRCm39) D765G possibly damaging Het
Parp3 C T 9: 106,351,704 (GRCm39) V170M possibly damaging Het
Pcdh15 A G 10: 74,471,504 (GRCm39) probably benign Het
Pcdha9 T G 18: 37,131,869 (GRCm39) S313A probably benign Het
Pfkm A G 15: 98,020,107 (GRCm39) R201G possibly damaging Het
Pgm5 G A 19: 24,727,765 (GRCm39) R375* probably null Het
Phactr2 A G 10: 13,349,809 (GRCm39) S72P possibly damaging Het
Plaat1 A T 16: 29,039,162 (GRCm39) R81* probably null Het
Plec A G 15: 76,058,732 (GRCm39) L3600P probably damaging Het
Pou6f1 G A 15: 100,483,874 (GRCm39) T208M possibly damaging Het
Rabep1 C T 11: 70,808,355 (GRCm39) S394L probably damaging Het
Ranbp2 T G 10: 58,301,489 (GRCm39) F687C probably damaging Het
Ranbp6 A G 19: 29,789,863 (GRCm39) F163S probably damaging Het
Rcor3 T C 1: 191,804,430 (GRCm39) N240D probably benign Het
Samd13 C A 3: 146,352,065 (GRCm39) K95N probably benign Het
Slc25a17 G T 15: 81,244,975 (GRCm39) probably benign Het
Slfn8 G T 11: 82,895,547 (GRCm39) H420N probably benign Het
Sptbn5 G A 2: 119,876,965 (GRCm39) probably benign Het
Stim2 G A 5: 54,267,075 (GRCm39) E21K probably damaging Het
Tmem163 A G 1: 127,479,067 (GRCm39) Y151H possibly damaging Het
Trio A G 15: 27,902,834 (GRCm39) I209T probably benign Het
Tubal3 T A 13: 3,983,432 (GRCm39) L404H probably damaging Het
Ubqln3 A G 7: 103,791,640 (GRCm39) F150S probably damaging Het
Ubr5 T C 15: 38,030,901 (GRCm39) S425G possibly damaging Het
Vmn2r52 T A 7: 9,904,861 (GRCm39) H326L probably 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
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
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'- ATGGCTGGCCGTTTCTTCAC -3'
(R):5'- TTTCAGCTCTCCAAGGAACC -3'

Sequencing Primer
(F):5'- GTTTCTTCACCCGCCTGCAG -3'
(R):5'- CCGAGGTTTCTTCGCAGCTG -3'
Posted On 2016-11-08