Incidental Mutation 'R1951:Ncam1'
ID 217311
Institutional Source Beutler Lab
Gene Symbol Ncam1
Ensembl Gene ENSMUSG00000039542
Gene Name neural cell adhesion molecule 1
Synonyms NCAM, NCAM-1, NCAM-120, E-NCAM, CD56, NCAM-140, NCAM-180
MMRRC Submission 039965-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.928) question?
Stock # R1951 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 49413436-49710225 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 49456492 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 486 (I486V)
Ref Sequence ENSEMBL: ENSMUSP00000141700 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000114476] [ENSMUST00000166811] [ENSMUST00000192584] [ENSMUST00000193547]
AlphaFold no structure available at present
Predicted Effect noncoding transcript
Transcript: ENSMUST00000068730
Predicted Effect probably benign
Transcript: ENSMUST00000114476
AA Change: I486V

PolyPhen 2 Score 0.206 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000110120
Gene: ENSMUSG00000039542
AA Change: I486V

DomainStartEndE-ValueType
IGc2 32 103 2.88e-4 SMART
IGc2 130 196 6.35e-6 SMART
IGc2 226 295 6.38e-20 SMART
IGc2 321 393 4.12e-14 SMART
IGc2 418 487 9.7e-11 SMART
FN3 501 586 4.77e-8 SMART
FN3 602 683 6.97e-1 SMART
low complexity region 711 725 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000166811
AA Change: I486V
SMART Domains Protein: ENSMUSP00000130668
Gene: ENSMUSG00000039542
AA Change: I486V

DomainStartEndE-ValueType
IGc2 32 103 2.88e-4 SMART
IGc2 130 196 6.35e-6 SMART
IGc2 226 295 6.38e-20 SMART
IGc2 321 393 4.12e-14 SMART
IGc2 418 487 9.7e-11 SMART
FN3 501 586 4.77e-8 SMART
FN3 602 683 6.97e-1 SMART
transmembrane domain 706 728 N/A INTRINSIC
low complexity region 797 809 N/A INTRINSIC
low complexity region 814 830 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192584
AA Change: I486V

PolyPhen 2 Score 0.356 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000141700
Gene: ENSMUSG00000039542
AA Change: I486V

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
IGc2 32 103 1.2e-6 SMART
IGc2 130 196 2.6e-8 SMART
IGc2 226 295 2.6e-22 SMART
IGc2 321 393 1.6e-16 SMART
IGc2 418 487 4e-13 SMART
FN3 501 586 2.4e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000193547
AA Change: I486V

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000142275
Gene: ENSMUSG00000039542
AA Change: I486V

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
IGc2 32 103 2.88e-4 SMART
IGc2 130 196 6.35e-6 SMART
IGc2 226 295 6.38e-20 SMART
IGc2 321 393 4.12e-14 SMART
IGc2 418 487 9.7e-11 SMART
FN3 501 586 4.77e-8 SMART
FN3 602 683 6.97e-1 SMART
transmembrane domain 706 728 N/A INTRINSIC
low complexity region 797 809 N/A INTRINSIC
low complexity region 814 830 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000194252
AA Change: I453V
Predicted Effect noncoding transcript
Transcript: ENSMUST00000215070
Predicted Effect noncoding transcript
Transcript: ENSMUST00000215465
Predicted Effect probably benign
Transcript: ENSMUST00000194844
Predicted Effect noncoding transcript
Transcript: ENSMUST00000216483
Meta Mutation Damage Score 0.2124 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.2%
Validation Efficiency 98% (84/86)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a cell adhesion protein which is a member of the immunoglobulin superfamily. The encoded protein is involved in cell-to-cell interactions as well as cell-matrix interactions during development and differentiation. The encoded protein has been shown to be involved in development of the nervous system, and for cells involved in the expansion of T cells and dendritic cells which play an important role in immune surveillance. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2011]
PHENOTYPE: Homozygous mutants show impairment in Morris water maze test, reduced brain and olfactory bulb size, hypoplasic corticospinal tract, abnormally distributed anterior pituitary cell types, and morphological and functional defects of neuromuscular junctions. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca15 C T 7: 119,960,655 (GRCm39) R706C probably damaging Het
Adcy3 T C 12: 4,258,624 (GRCm39) F847S probably benign Het
Alyref C G 11: 120,486,758 (GRCm39) V168L probably damaging Het
Arhgap28 G A 17: 68,208,336 (GRCm39) A44V probably benign Het
Asap3 C T 4: 135,954,767 (GRCm39) R60* probably null Het
Baz1b T A 5: 135,245,593 (GRCm39) N347K probably benign Het
Best2 T A 8: 85,737,858 (GRCm39) N179I possibly damaging Het
Bfar C T 16: 13,519,970 (GRCm39) S276L probably damaging Het
Bloc1s3 A G 7: 19,241,483 (GRCm39) V15A possibly damaging Het
Borcs5 A G 6: 134,687,230 (GRCm39) H196R unknown Het
Calhm3 A G 19: 47,140,256 (GRCm39) L279P probably benign Het
Cand1 A T 10: 119,043,925 (GRCm39) probably benign Het
Car15 T C 16: 17,655,269 (GRCm39) D57G possibly damaging Het
Casp12 G A 9: 5,348,959 (GRCm39) probably null Het
Cd93 T C 2: 148,283,778 (GRCm39) T523A probably benign Het
Ces4a G A 8: 105,864,729 (GRCm39) G69S probably damaging Het
Ckap5 A G 2: 91,386,837 (GRCm39) probably benign Het
Col6a5 G A 9: 105,814,156 (GRCm39) R619W unknown Het
Colec12 G A 18: 9,859,975 (GRCm39) probably null Het
Crmp1 G A 5: 37,430,699 (GRCm39) V222I possibly damaging Het
Crnkl1 G A 2: 145,770,120 (GRCm39) A241V probably damaging Het
Ctbp2 A G 7: 132,616,756 (GRCm39) S60P probably benign Het
Cyp2c68 T C 19: 39,700,972 (GRCm39) Y282C probably benign Het
Dhx36 T C 3: 62,391,694 (GRCm39) I551V probably damaging Het
Dlg5 T A 14: 24,206,537 (GRCm39) probably benign Het
Dlgap1 A T 17: 71,068,306 (GRCm39) I300F probably damaging Het
Dmd T A X: 82,874,123 (GRCm39) I1342N probably damaging Het
Dnah6 T A 6: 73,061,704 (GRCm39) R2794* probably null Het
Fcgr1 G A 3: 96,194,386 (GRCm39) T167I probably damaging Het
Fgl1 G T 8: 41,650,387 (GRCm39) F187L probably benign Het
Fras1 T A 5: 96,860,242 (GRCm39) V2096E probably benign Het
Gm10647 A G 9: 66,705,762 (GRCm39) probably benign Het
Gm14226 G A 2: 154,866,255 (GRCm39) D71N possibly damaging Het
Grip2 A T 6: 91,760,829 (GRCm39) I284N probably damaging Het
Hirip3 A G 7: 126,462,038 (GRCm39) R19G probably damaging Het
Ift70b A G 2: 75,767,586 (GRCm39) L389P probably damaging Het
Irx5 A G 8: 93,086,438 (GRCm39) N174D probably damaging Het
Itgal A G 7: 126,929,317 (GRCm39) D1078G probably damaging Het
Khdc3 T C 9: 73,010,519 (GRCm39) V123A possibly damaging Het
Klhl13 A G X: 23,127,820 (GRCm39) probably benign Het
Klhl42 T C 6: 146,993,321 (GRCm39) S98P probably damaging Het
Lrp5 T C 19: 3,670,298 (GRCm39) N602S possibly damaging Het
Lrrd1 A T 5: 3,901,488 (GRCm39) I598F probably damaging Het
Ltbp1 A G 17: 75,458,372 (GRCm39) T318A probably benign Het
Mfsd6 A G 1: 52,748,517 (GRCm39) F116S probably damaging Het
Nptx1 A G 11: 119,434,006 (GRCm39) probably null Het
Nrg1 T C 8: 32,408,221 (GRCm39) Y4C probably damaging Het
Nsf G A 11: 103,773,702 (GRCm39) R271* probably null Het
Or5d39 A G 2: 87,979,641 (GRCm39) S241P possibly damaging Het
Or8g24 T A 9: 38,989,580 (GRCm39) I154F probably benign Het
Or8k18 G C 2: 86,085,440 (GRCm39) T199S probably benign Het
Or8k21 T A 2: 86,145,504 (GRCm39) N42I probably damaging Het
Or8k24 A T 2: 86,215,855 (GRCm39) H302Q probably benign Het
Pax2 A G 19: 44,777,271 (GRCm39) T155A probably benign Het
Pdia4 A G 6: 47,780,813 (GRCm39) Y212H probably damaging Het
Pgr A G 9: 8,946,954 (GRCm39) probably benign Het
Pitpnm3 G T 11: 71,965,450 (GRCm39) H112N possibly damaging Het
Ppargc1b G T 18: 61,431,848 (GRCm39) T1000K possibly damaging Het
Psd3 C A 8: 68,416,139 (GRCm39) C586F probably benign Het
Ptprm A T 17: 67,247,575 (GRCm39) S587T probably benign Het
Rabep2 A T 7: 126,037,736 (GRCm39) R169S possibly damaging Het
Rad21l T C 2: 151,497,179 (GRCm39) R309G probably benign Het
Rbm12 T C 2: 155,939,133 (GRCm39) R380G probably damaging Het
Selp A G 1: 163,954,081 (GRCm39) N127S probably benign Het
Slc12a2 A G 18: 58,012,467 (GRCm39) T197A possibly damaging Het
Slc22a18 C T 7: 143,029,984 (GRCm39) T17I probably damaging Het
Sptbn4 T C 7: 27,065,868 (GRCm39) E2026G possibly damaging Het
Srf A T 17: 46,862,633 (GRCm39) M285K possibly damaging Het
Tanc1 T C 2: 59,622,156 (GRCm39) V425A possibly damaging Het
Tle4 A T 19: 14,493,721 (GRCm39) probably null Het
Tmem132e A G 11: 82,335,908 (GRCm39) R905G possibly damaging Het
Tmem200c A T 17: 69,147,983 (GRCm39) I189F probably damaging Het
Trappc13 T C 13: 104,311,150 (GRCm39) Q87R probably benign Het
Trpm7 A T 2: 126,673,219 (GRCm39) D511E probably damaging Het
Ttn A T 2: 76,632,634 (GRCm39) I14140N possibly damaging Het
Virma A G 4: 11,513,907 (GRCm39) D587G probably benign Het
Vmn1r72 A G 7: 11,403,731 (GRCm39) L239P probably damaging Het
Vmn2r68 A G 7: 84,883,102 (GRCm39) F217L probably damaging Het
Vps13c T C 9: 67,881,041 (GRCm39) probably null Het
Vrtn T C 12: 84,695,973 (GRCm39) V241A probably damaging Het
Xdh T C 17: 74,214,653 (GRCm39) E764G probably damaging Het
Zranb3 A T 1: 127,927,136 (GRCm39) V343D probably damaging Het
Other mutations in Ncam1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00592:Ncam1 APN 9 49,434,865 (GRCm39) missense probably damaging 1.00
IGL01384:Ncam1 APN 9 49,421,152 (GRCm39) missense possibly damaging 0.76
IGL01798:Ncam1 APN 9 49,419,907 (GRCm39) missense probably damaging 1.00
IGL02239:Ncam1 APN 9 49,478,702 (GRCm39) missense probably damaging 1.00
IGL02368:Ncam1 APN 9 49,454,383 (GRCm39) nonsense probably null
IGL02616:Ncam1 APN 9 49,419,988 (GRCm39) missense probably benign 0.23
PIT4431001:Ncam1 UTSW 9 49,709,993 (GRCm39) missense probably benign 0.04
R0164:Ncam1 UTSW 9 49,479,709 (GRCm39) missense probably damaging 1.00
R0164:Ncam1 UTSW 9 49,479,709 (GRCm39) missense probably damaging 1.00
R0502:Ncam1 UTSW 9 49,481,118 (GRCm39) unclassified probably benign
R0924:Ncam1 UTSW 9 49,473,476 (GRCm39) intron probably benign
R1398:Ncam1 UTSW 9 49,428,889 (GRCm39) intron probably benign
R1440:Ncam1 UTSW 9 49,456,100 (GRCm39) missense probably damaging 1.00
R1491:Ncam1 UTSW 9 49,416,849 (GRCm39) missense probably benign 0.15
R1676:Ncam1 UTSW 9 49,468,472 (GRCm39) missense probably damaging 1.00
R1743:Ncam1 UTSW 9 49,468,445 (GRCm39) missense probably damaging 1.00
R1769:Ncam1 UTSW 9 49,456,556 (GRCm39) unclassified probably benign
R2143:Ncam1 UTSW 9 49,454,319 (GRCm39) missense possibly damaging 0.87
R2167:Ncam1 UTSW 9 49,479,781 (GRCm39) missense probably benign 0.42
R2170:Ncam1 UTSW 9 49,709,981 (GRCm39) missense probably benign 0.06
R2290:Ncam1 UTSW 9 49,434,951 (GRCm39) splice site probably benign
R2321:Ncam1 UTSW 9 49,456,132 (GRCm39) unclassified probably benign
R3001:Ncam1 UTSW 9 49,468,526 (GRCm39) missense probably damaging 0.99
R3002:Ncam1 UTSW 9 49,468,526 (GRCm39) missense probably damaging 0.99
R4026:Ncam1 UTSW 9 49,476,295 (GRCm39) missense probably benign 0.00
R4279:Ncam1 UTSW 9 49,418,259 (GRCm39) intron probably benign
R4289:Ncam1 UTSW 9 49,468,472 (GRCm39) missense probably damaging 1.00
R4873:Ncam1 UTSW 9 49,418,921 (GRCm39) intron probably benign
R4875:Ncam1 UTSW 9 49,418,921 (GRCm39) intron probably benign
R4883:Ncam1 UTSW 9 49,453,183 (GRCm39) splice site probably null
R4899:Ncam1 UTSW 9 49,456,551 (GRCm39) critical splice acceptor site probably null
R4923:Ncam1 UTSW 9 49,416,779 (GRCm39) missense probably benign
R5041:Ncam1 UTSW 9 49,478,085 (GRCm39) missense probably damaging 1.00
R5058:Ncam1 UTSW 9 49,709,995 (GRCm39) missense probably benign 0.16
R5386:Ncam1 UTSW 9 49,476,174 (GRCm39) missense probably damaging 1.00
R5388:Ncam1 UTSW 9 49,456,054 (GRCm39) missense probably benign
R5512:Ncam1 UTSW 9 49,420,999 (GRCm39) splice site probably null
R5598:Ncam1 UTSW 9 49,457,051 (GRCm39) missense probably damaging 1.00
R5895:Ncam1 UTSW 9 49,418,343 (GRCm39) missense probably benign
R5972:Ncam1 UTSW 9 49,418,829 (GRCm39) missense possibly damaging 0.93
R6059:Ncam1 UTSW 9 49,455,966 (GRCm39) missense probably damaging 1.00
R6226:Ncam1 UTSW 9 49,476,304 (GRCm39) missense probably benign 0.00
R6392:Ncam1 UTSW 9 49,434,875 (GRCm39) missense probably damaging 0.99
R6750:Ncam1 UTSW 9 49,478,639 (GRCm39) missense probably damaging 1.00
R6799:Ncam1 UTSW 9 49,419,911 (GRCm39) missense probably damaging 0.99
R7230:Ncam1 UTSW 9 49,421,123 (GRCm39) missense probably benign 0.00
R7335:Ncam1 UTSW 9 49,418,211 (GRCm39) missense
R7561:Ncam1 UTSW 9 49,476,242 (GRCm39) missense probably damaging 1.00
R7645:Ncam1 UTSW 9 49,476,303 (GRCm39) missense probably benign 0.01
R8022:Ncam1 UTSW 9 49,476,192 (GRCm39) missense possibly damaging 0.72
R8023:Ncam1 UTSW 9 49,421,057 (GRCm39) missense probably benign 0.00
R8045:Ncam1 UTSW 9 49,418,736 (GRCm39) missense
R8234:Ncam1 UTSW 9 49,456,523 (GRCm39) missense probably damaging 0.99
R8308:Ncam1 UTSW 9 49,479,817 (GRCm39) missense probably damaging 0.99
R8370:Ncam1 UTSW 9 49,468,431 (GRCm39) nonsense probably null
R8500:Ncam1 UTSW 9 49,431,445 (GRCm39) missense probably damaging 1.00
R8542:Ncam1 UTSW 9 49,419,898 (GRCm39) missense probably damaging 1.00
R8944:Ncam1 UTSW 9 49,431,493 (GRCm39) missense probably damaging 1.00
R8977:Ncam1 UTSW 9 49,418,825 (GRCm39) missense probably damaging 1.00
R9028:Ncam1 UTSW 9 49,418,736 (GRCm39) missense
R9034:Ncam1 UTSW 9 49,481,198 (GRCm39) missense probably benign 0.42
R9106:Ncam1 UTSW 9 49,428,856 (GRCm39) missense probably damaging 0.99
R9224:Ncam1 UTSW 9 49,419,995 (GRCm39) missense probably damaging 1.00
R9330:Ncam1 UTSW 9 49,456,097 (GRCm39) missense probably benign
X0062:Ncam1 UTSW 9 49,456,901 (GRCm39) nonsense probably null
X0064:Ncam1 UTSW 9 49,477,980 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGGAGACTCCACTTTCGTAGC -3'
(R):5'- ACACTGAGCTCCTTCCACTG -3'

Sequencing Primer
(F):5'- GATGGATTCTCTCTCACTCTAAGTTG -3'
(R):5'- ACTGAGCTCCTTCCACTGAGATAG -3'
Posted On 2014-08-01