Incidental Mutation 'R9208:Ncdn'
ID 698624
Institutional Source Beutler Lab
Gene Symbol Ncdn
Ensembl Gene ENSMUSG00000028833
Gene Name neurochondrin
Synonyms neurochondrin-2, neurochondrin-1, norbin
MMRRC Submission 068982-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9208 (G1)
Quality Score 225.009
Status Validated
Chromosome 4
Chromosomal Location 126637543-126647231 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 126644041 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 260 (D260E)
Ref Sequence ENSEMBL: ENSMUSP00000030637 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030637] [ENSMUST00000047431] [ENSMUST00000102607] [ENSMUST00000102608] [ENSMUST00000106116] [ENSMUST00000132660] [ENSMUST00000148935] [ENSMUST00000154640]
AlphaFold Q9Z0E0
Predicted Effect probably benign
Transcript: ENSMUST00000030637
AA Change: D260E

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: D260E

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 benign
Transcript: ENSMUST00000106116
AA Change: D260E

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: D260E

DomainStartEndE-ValueType
Pfam:Neurochondrin 30 637 9.1e-217 PFAM
low complexity region 649 659 N/A INTRINSIC
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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.4%
Validation Efficiency 98% (65/66)
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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acot6 T A 12: 84,153,358 (GRCm39) L200Q possibly damaging Het
Apbb1 A G 7: 105,208,727 (GRCm39) S569P probably damaging Het
Atl3 A G 19: 7,487,447 (GRCm39) I121V probably benign Het
C87436 A G 6: 86,423,227 (GRCm39) D267G probably benign Het
Ccdc7a T A 8: 129,472,482 (GRCm39) I1617F possibly damaging Het
Cic T C 7: 24,987,502 (GRCm39) F1397L probably benign Het
Cln6 T A 9: 62,756,465 (GRCm39) M203K probably benign Het
Clock A G 5: 76,384,871 (GRCm39) S449P probably benign Het
Cse1l C A 2: 166,783,185 (GRCm39) N743K probably damaging Het
Cyp1a2 A G 9: 57,589,583 (GRCm39) I77T probably damaging Het
D6Wsu163e A G 6: 126,943,932 (GRCm39) I443V probably benign Het
Dctn1 T C 6: 83,176,684 (GRCm39) V1246A probably benign Het
Dennd5b T C 6: 149,002,698 (GRCm39) E37G probably benign Het
Dnah11 C T 12: 117,991,251 (GRCm39) E2372K probably damaging Het
Ecpas A T 4: 58,875,444 (GRCm39) D173E probably damaging Het
Ercc5 T C 1: 44,217,503 (GRCm39) W949R possibly damaging Het
Fam13c A G 10: 70,388,869 (GRCm39) E465G probably damaging Het
Fam83d T A 2: 158,610,466 (GRCm39) C145S probably damaging Het
Fbln7 T A 2: 128,737,343 (GRCm39) V386E probably damaging Het
Fpr3 A T 17: 18,191,131 (GRCm39) Q134L probably damaging Het
Gm3636 T A 14: 17,955,001 (GRCm39) R5S possibly damaging Het
Gna15 A G 10: 81,345,224 (GRCm39) S214P probably benign Het
Hdac9 A G 12: 34,220,101 (GRCm39) M897T probably benign Het
Hdc T C 2: 126,436,600 (GRCm39) N424D probably benign Het
Krtap27-1 A G 16: 88,468,316 (GRCm39) V76A possibly damaging Het
Lrrd1 T A 5: 3,900,995 (GRCm39) H433Q probably damaging Het
Ltn1 T C 16: 87,197,298 (GRCm39) D1180G probably benign Het
Macf1 A G 4: 123,577,925 (GRCm39) C20R unknown Het
Mphosph9 T C 5: 124,450,854 (GRCm39) N306D probably damaging Het
Mpp7 T C 18: 7,403,327 (GRCm39) R328G probably benign Het
Mslnl C T 17: 25,961,694 (GRCm39) P117S possibly damaging Het
Muc16 T A 9: 18,419,833 (GRCm39) K117M probably damaging Het
Mycbp2 T C 14: 103,532,664 (GRCm39) N430S probably benign Het
Myl1 T C 1: 66,973,683 (GRCm39) I8V probably benign Het
Nkx3-2 T A 5: 41,919,114 (GRCm39) R291S probably damaging Het
Nr4a2 A G 2: 56,999,093 (GRCm39) V448A probably damaging Het
Nrip1 T C 16: 76,089,616 (GRCm39) E647G possibly damaging Het
Or4c12 C A 2: 89,773,725 (GRCm39) V245L possibly damaging Het
Or52a5b A G 7: 103,417,478 (GRCm39) I42T probably benign Het
Or8c14-ps1 T C 9: 38,101,120 (GRCm39) M33T possibly damaging Het
Or8s10 C A 15: 98,335,614 (GRCm39) A88E probably benign Het
Patj A T 4: 98,427,310 (GRCm39) I172F unknown Het
Per1 T C 11: 68,995,636 (GRCm39) S739P possibly damaging Het
Plekhn1 A C 4: 156,306,859 (GRCm39) V510G possibly damaging Het
Plxna4 A T 6: 32,494,379 (GRCm39) V79D probably damaging Het
Pram1 A G 17: 33,859,801 (GRCm39) T123A probably benign Het
Ptpn23 C A 9: 110,237,101 (GRCm39) probably null Het
Rcbtb2 C T 14: 73,414,500 (GRCm39) S437L probably damaging Het
Resf1 C T 6: 149,228,027 (GRCm39) L358F probably damaging Het
Rxfp4 T A 3: 88,559,390 (GRCm39) R354* probably null Het
Serpinb5 A G 1: 106,803,853 (GRCm39) T180A probably damaging Het
Slc7a14 T A 3: 31,281,359 (GRCm39) D317V probably damaging Het
Slco5a1 A G 1: 13,059,802 (GRCm39) probably null Het
Snx14 T A 9: 88,265,832 (GRCm39) T768S probably benign Het
Sorbs1 T A 19: 40,353,462 (GRCm39) probably benign Het
Stambp C T 6: 83,528,954 (GRCm39) A364T probably damaging Het
Tgm3 T A 2: 129,865,618 (GRCm39) I6N possibly damaging Het
Tmem106b A T 6: 13,082,430 (GRCm39) T202S probably damaging Het
Tnfsf8 A G 4: 63,752,450 (GRCm39) V205A probably benign Het
Treml2 A T 17: 48,614,922 (GRCm39) R136* probably null Het
Trim46 T C 3: 89,142,466 (GRCm39) T674A possibly damaging Het
Trmt13 T A 3: 116,376,356 (GRCm39) Y345F possibly damaging Het
Tspyl4 A G 10: 34,173,568 (GRCm39) H20R probably benign Het
Uvssa T C 5: 33,571,419 (GRCm39) probably null Het
Vmn1r192 A T 13: 22,371,401 (GRCm39) F273Y probably damaging Het
Vmn2r45 A T 7: 8,486,298 (GRCm39) I330N probably damaging Het
Zfp40 A G 17: 23,394,551 (GRCm39) F679L 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
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
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'- ATAAGGGCATAGCAGGCTGTTAC -3'
(R):5'- ATGGCTACGGCTTTGACCAG -3'

Sequencing Primer
(F):5'- ATAGCAGGCTGTTACCACGTC -3'
(R):5'- TACGGCTTTGACCAGGCTCTG -3'
Posted On 2022-02-07