Incidental Mutation 'R5058:Ncam1'
ID 391030
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 042648-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.928) question?
Stock # R5058 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 49413436-49710225 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 49709995 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Cysteine at position 12 (F12C)
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 probably benign
Transcript: ENSMUST00000114476
AA Change: F12C

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000110120
Gene: ENSMUSG00000039542
AA Change: F12C

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 probably benign
Transcript: ENSMUST00000166811
AA Change: F12C

PolyPhen 2 Score 0.035 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000130668
Gene: ENSMUSG00000039542
AA Change: F12C

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: F12C

PolyPhen 2 Score 0.163 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000141700
Gene: ENSMUSG00000039542
AA Change: F12C

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: F12C

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000142275
Gene: ENSMUSG00000039542
AA Change: F12C

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 noncoding transcript
Transcript: ENSMUST00000217121
Meta Mutation Damage Score 0.0834 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.3%
  • 20x: 92.2%
Validation Efficiency 100% (79/79)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adprhl1 T C 8: 13,292,625 (GRCm39) Y222C probably damaging Het
Adprs A G 4: 126,212,238 (GRCm39) S94P probably damaging Het
Atp11b A G 3: 35,863,510 (GRCm39) E202G probably benign Het
Cacna1d G T 14: 29,836,201 (GRCm39) S849* probably null Het
Camsap1 T C 2: 25,829,375 (GRCm39) D783G probably benign Het
Cbfa2t2 T A 2: 154,346,665 (GRCm39) I124N probably damaging Het
Ccdc13 A T 9: 121,646,613 (GRCm39) probably benign Het
Cfap44 G A 16: 44,240,567 (GRCm39) probably null Het
Col17a1 C A 19: 47,673,989 (GRCm39) E13* probably null Het
Cybb C G X: 9,316,989 (GRCm39) D246H probably benign Het
Dennd6b A G 15: 89,071,553 (GRCm39) L288P possibly damaging Het
Dhx37 A C 5: 125,499,295 (GRCm39) Y638D probably benign Het
Epb41 G A 4: 131,734,746 (GRCm39) probably benign Het
Esp31 A T 17: 38,955,500 (GRCm39) I48L possibly damaging Het
Fat3 T C 9: 15,908,154 (GRCm39) Q2616R probably damaging Het
Fbxo33 A G 12: 59,265,919 (GRCm39) I116T probably benign Het
Flnb G T 14: 7,924,262 (GRCm38) E1792* probably null Het
Fzd2 G A 11: 102,495,633 (GRCm39) G26R probably damaging Het
Gm11677 T A 11: 111,616,264 (GRCm39) noncoding transcript Het
Gm7137 A T 10: 77,623,905 (GRCm39) probably benign Het
Hnrnpr A G 4: 136,063,648 (GRCm39) T252A possibly damaging Het
Hyal5 T C 6: 24,891,484 (GRCm39) F433L probably damaging Het
Kcnmb4 T A 10: 116,299,833 (GRCm39) probably benign Het
Meltf A G 16: 31,706,421 (GRCm39) probably null Het
Mllt6 G A 11: 97,560,326 (GRCm39) S210N possibly damaging Het
Muc6 T C 7: 141,230,491 (GRCm39) D1213G probably benign Het
Nfxl1 A T 5: 72,713,582 (GRCm39) D120E probably benign Het
Nrg1 T C 8: 32,314,587 (GRCm39) Q142R probably damaging Het
Or10c1 A G 17: 37,522,558 (GRCm39) L62P probably damaging Het
Or1j18 T G 2: 36,625,011 (GRCm39) L226R possibly damaging Het
Or2h15 G A 17: 38,441,432 (GRCm39) S217F probably damaging Het
Or56a4 T C 7: 104,806,355 (GRCm39) N178S probably damaging Het
Or5k16 T C 16: 58,736,435 (GRCm39) T190A probably benign Het
Or8c10 C A 9: 38,279,220 (GRCm39) T116K probably damaging Het
Or8g30 C A 9: 39,229,960 (GRCm39) V317L probably benign Het
Or9s18 C A 13: 65,300,743 (GRCm39) A235D possibly damaging Het
Padi2 G T 4: 140,659,432 (GRCm39) V246L probably benign Het
Pgghg C T 7: 140,522,455 (GRCm39) T63I possibly damaging Het
Pitpnm1 A G 19: 4,162,758 (GRCm39) N1117S probably benign Het
Plch1 G T 3: 63,630,202 (GRCm39) T534K probably damaging Het
Poc1a G T 9: 106,227,012 (GRCm39) probably benign Het
Polr3c T C 3: 96,630,833 (GRCm39) I196V probably benign Het
Prph A T 15: 98,953,113 (GRCm39) probably benign Het
Ptprg C A 14: 12,037,387 (GRCm38) T189K possibly damaging Het
R3hcc1 A T 14: 69,941,463 (GRCm39) I183N probably damaging Het
Rundc1 T C 11: 101,316,363 (GRCm39) L145P probably benign Het
Slc26a3 A G 12: 31,520,964 (GRCm39) K723E possibly damaging Het
Slc38a3 T C 9: 107,536,390 (GRCm39) E2G possibly damaging Het
Slc9a5 G T 8: 106,082,490 (GRCm39) V252L probably benign Het
Smim26 C T 2: 144,437,043 (GRCm39) T64M probably benign Het
Socs4 C T 14: 47,527,589 (GRCm39) R175* probably null Het
Srebf2 T C 15: 82,066,251 (GRCm39) S600P probably damaging Het
Tas2r107 A T 6: 131,636,705 (GRCm39) S115T probably damaging Het
Tenm2 T C 11: 36,097,907 (GRCm39) D447G possibly damaging Het
Thbs2 T A 17: 14,896,591 (GRCm39) D766V probably damaging Het
Tinagl1 A G 4: 130,061,250 (GRCm39) V300A probably benign Het
Tle6 T A 10: 81,430,072 (GRCm39) N332I possibly damaging Het
Tle6 C A 10: 81,431,791 (GRCm39) W151L probably damaging Het
Tnfrsf13c C T 15: 82,108,408 (GRCm39) V36M probably damaging Het
Tns2 T C 15: 102,016,295 (GRCm39) I211T possibly damaging Het
Trp63 A G 16: 25,701,344 (GRCm39) N379D probably damaging Het
Trpc2 T C 7: 101,738,316 (GRCm39) W433R probably damaging Het
Tyw1 T A 5: 130,305,927 (GRCm39) L350Q probably benign Het
Usf3 T C 16: 44,033,070 (GRCm39) L76P probably damaging Het
Vmn2r79 T C 7: 86,651,423 (GRCm39) L274P 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
R1951:Ncam1 UTSW 9 49,456,492 (GRCm39) missense probably benign 0.36
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
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'- CCTTCTCAGCTCAGTGAAAATG -3'
(R):5'- GGACTGTCACTCATTCTCCG -3'

Sequencing Primer
(F):5'- CTCAGCTCAGTGAAAATGCTGTC -3'
(R):5'- TGGCTGGCAAGAAACAATTCTGC -3'
Posted On 2016-06-06