Incidental Mutation 'R1789:Ncdn'
ID 201600
Institutional Source Beutler Lab
Gene Symbol Ncdn
Ensembl Gene ENSMUSG00000028833
Gene Name neurochondrin
Synonyms neurochondrin-2, neurochondrin-1, norbin
MMRRC Submission 039820-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1789 (G1)
Quality Score 146
Status Not validated
Chromosome 4
Chromosomal Location 126637543-126647231 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 126645796 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Cysteine at position 38 (R38C)
Ref Sequence ENSEMBL: ENSMUSP00000101722 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030637] [ENSMUST00000047431] [ENSMUST00000102607] [ENSMUST00000102608] [ENSMUST00000106116] [ENSMUST00000154640] [ENSMUST00000148935] [ENSMUST00000132660]
AlphaFold Q9Z0E0
Predicted Effect probably damaging
Transcript: ENSMUST00000030637
AA Change: R38C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: R38C

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 damaging
Transcript: ENSMUST00000106116
AA Change: R38C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: R38C

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: ENSMUST00000154640
SMART Domains Protein: ENSMUSP00000122352
Gene: ENSMUSG00000028830

DomainStartEndE-ValueType
low complexity region 83 97 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000148935
Predicted Effect probably benign
Transcript: ENSMUST00000132660
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.2%
  • 20x: 92.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a 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: 100 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc5 G A 16: 20,184,701 (GRCm39) P986L probably damaging Het
Acad10 A T 5: 121,769,456 (GRCm39) Y667N possibly damaging Het
Ahi1 G A 10: 20,839,014 (GRCm39) G121D probably benign Het
Ampd1 T A 3: 103,006,442 (GRCm39) I690N possibly damaging Het
Amy1 C A 3: 113,351,814 (GRCm39) W425L possibly damaging Het
Arhgap27 A T 11: 103,223,831 (GRCm39) V823E probably damaging Het
Arhgef17 A G 7: 100,579,077 (GRCm39) S624P probably damaging Het
Arid5b T C 10: 68,021,897 (GRCm39) H231R probably damaging Het
Aspscr1 C A 11: 120,579,386 (GRCm39) T78N probably damaging Het
Auts2 T A 5: 131,501,288 (GRCm39) T42S probably damaging Het
Ccdc171 A G 4: 83,473,045 (GRCm39) D158G probably damaging Het
Ces4a G A 8: 105,864,729 (GRCm39) G69S probably damaging Het
Cfap61 T C 2: 145,781,913 (GRCm39) probably null Het
Chrna5 T C 9: 54,911,935 (GRCm39) V245A possibly damaging Het
Cntnap5c G A 17: 58,320,916 (GRCm39) G163R probably damaging Het
Col5a2 A G 1: 45,417,465 (GRCm39) probably null Het
Col5a2 T C 1: 45,433,936 (GRCm39) Q759R probably damaging Het
Comp A G 8: 70,829,796 (GRCm39) D340G probably benign Het
Cyfip1 T A 7: 55,576,143 (GRCm39) D1104E probably damaging Het
Dnah11 A T 12: 118,002,515 (GRCm39) S308T probably damaging Het
Dnah5 A G 15: 28,270,572 (GRCm39) H958R probably benign Het
Elp3 A G 14: 65,785,368 (GRCm39) Y478H probably damaging Het
Fam237b A T 5: 5,625,652 (GRCm39) Q116L possibly damaging Het
Fat3 T C 9: 16,288,281 (GRCm39) Y414C probably benign Het
Fbxo10 C A 4: 45,046,389 (GRCm39) A574S probably damaging Het
Fsip2 G T 2: 82,807,906 (GRCm39) L1408F probably benign Het
Fubp3 T C 2: 31,501,747 (GRCm39) V425A possibly damaging Het
Gm7168 A T 17: 14,169,846 (GRCm39) R404S probably benign Het
Gpd1 T G 15: 99,621,083 (GRCm39) F299C probably damaging Het
Gpr137 C T 19: 6,919,425 (GRCm39) probably benign Het
Grin3b T C 10: 79,809,242 (GRCm39) S331P probably benign Het
Grk3 T A 5: 113,089,584 (GRCm39) I281F probably damaging Het
Hoxb7 T A 11: 96,177,607 (GRCm39) S18R probably damaging Het
Igf1r C T 7: 67,864,681 (GRCm39) R1160* probably null Het
Itfg1 A G 8: 86,452,141 (GRCm39) probably null Het
Itgb8 T C 12: 119,166,190 (GRCm39) I114V probably benign Het
Kcnk1 A G 8: 126,752,123 (GRCm39) E243G possibly damaging Het
Kif27 A G 13: 58,491,822 (GRCm39) L439P probably damaging Het
Kif2c T A 4: 117,024,558 (GRCm39) Q279L probably benign Het
Kmt2d A T 15: 98,749,955 (GRCm39) probably benign Het
L3mbtl1 A G 2: 162,816,422 (GRCm39) T821A probably benign Het
Lrrc24 A T 15: 76,606,778 (GRCm39) M206K probably benign Het
Mamdc4 T G 2: 25,457,634 (GRCm39) K460Q possibly damaging Het
Maml2 C G 9: 13,608,641 (GRCm39) L30V probably damaging Het
Mc5r C G 18: 68,471,741 (GRCm39) probably null Het
Myo10 T G 15: 25,726,611 (GRCm39) probably null Het
Myo1e T A 9: 70,246,066 (GRCm39) L419Q probably damaging Het
Myo6 C A 9: 80,207,854 (GRCm39) H1115Q probably damaging Het
Myo7a A G 7: 97,756,302 (GRCm39) V10A probably damaging Het
Myoz2 C T 3: 122,819,776 (GRCm39) R61H probably damaging Het
Nckap1 T A 2: 80,350,900 (GRCm39) T736S probably benign Het
Ncor2 G A 5: 125,096,954 (GRCm39) A2325V probably damaging Het
Nid2 T A 14: 19,802,499 (GRCm39) V140E possibly damaging Het
Nlrp9c C A 7: 26,079,915 (GRCm39) D704Y probably benign Het
Notch3 T A 17: 32,377,699 (GRCm39) S126C probably damaging Het
Or2g7 T C 17: 38,378,839 (GRCm39) I259T probably damaging Het
Or5p60 A G 7: 107,724,122 (GRCm39) F116S probably benign Het
Or5w10 A T 2: 87,375,327 (GRCm39) L187H probably damaging Het
Or6c219 A T 10: 129,781,451 (GRCm39) L160* probably null Het
Or6c6c T C 10: 129,541,476 (GRCm39) M243T possibly damaging Het
Or6d15 A C 6: 116,559,658 (GRCm39) F83C probably damaging Het
Pdzd7 A G 19: 45,027,667 (GRCm39) I269T probably damaging Het
Phf3 A T 1: 30,845,287 (GRCm39) D1299E probably damaging Het
Pitx2 T A 3: 129,012,403 (GRCm39) Y271N probably damaging Het
Polk T C 13: 96,633,140 (GRCm39) E301G probably damaging Het
Prkdc C A 16: 15,557,388 (GRCm39) N2230K probably damaging Het
Prlr A G 15: 10,322,622 (GRCm39) E170G probably benign Het
Prss55 A G 14: 64,313,179 (GRCm39) I235T probably damaging Het
Psd3 T C 8: 68,413,217 (GRCm39) I724V probably benign Het
Rabep2 A G 7: 126,037,971 (GRCm39) T248A possibly damaging Het
Rbm26 T A 14: 105,354,509 (GRCm39) K949N probably benign Het
Rnf213 T A 11: 119,331,047 (GRCm39) D2085E probably damaging Het
Serpinb7 A T 1: 107,378,003 (GRCm39) H232L possibly damaging Het
Slu7 A G 11: 43,336,069 (GRCm39) Q484R probably benign Het
Smg1 A G 7: 117,745,021 (GRCm39) S3044P possibly damaging Het
Snrnp48 A G 13: 38,405,336 (GRCm39) D248G possibly damaging Het
Snrpc C A 17: 28,064,193 (GRCm39) P66Q unknown Het
Snrpn T A 7: 59,633,207 (GRCm39) probably benign Het
Spag17 T A 3: 99,846,672 (GRCm39) S65R possibly damaging Het
Srsf6 C A 2: 162,776,408 (GRCm39) probably benign Het
Stil T A 4: 114,898,979 (GRCm39) M1203K probably benign Het
Syt17 T C 7: 118,036,061 (GRCm39) T106A probably benign Het
Tbx15 C T 3: 99,259,562 (GRCm39) Q478* probably null Het
Tg A T 15: 66,609,397 (GRCm39) Q319L probably benign Het
Thada A G 17: 84,755,461 (GRCm39) L243P probably damaging Het
Thada G T 17: 84,755,462 (GRCm39) L243I probably damaging Het
Tnnt3 A G 7: 142,066,101 (GRCm39) R211G probably damaging Het
Togaram1 A T 12: 65,049,409 (GRCm39) Q1282L possibly damaging Het
Tpm3-rs7 T G 14: 113,552,379 (GRCm39) M91R probably damaging Het
Trappc9 G A 15: 72,897,816 (GRCm39) R377W probably damaging Het
Ttll7 T G 3: 146,621,535 (GRCm39) L378R probably damaging Het
Tyw1 T G 5: 130,287,834 (GRCm39) I22R probably damaging Het
Ubr3 T C 2: 69,846,711 (GRCm39) S1645P possibly damaging Het
Ubr4 T C 4: 139,120,364 (GRCm39) L263P probably damaging Het
Unc13c T C 9: 73,663,621 (GRCm39) E1071G possibly damaging Het
Vmn2r44 G T 7: 8,383,122 (GRCm39) D157E possibly damaging Het
Vps16 C T 2: 130,285,520 (GRCm39) T821I probably benign Het
Washc4 T C 10: 83,415,389 (GRCm39) V793A possibly damaging Het
Wdr35 G T 12: 9,027,435 (GRCm39) probably null Het
Zfp277 A G 12: 40,414,084 (GRCm39) F254L 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
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
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'- CAAAGGTAGAGGTCTCAGGC -3'
(R):5'- GTCAGTCATGAGGAAGCCAC -3'

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