Incidental Mutation 'R3838:Clstn1'
ID 276982
Institutional Source Beutler Lab
Gene Symbol Clstn1
Ensembl Gene ENSMUSG00000039953
Gene Name calsyntenin 1
Synonyms Cst-1, alcadein alpha, calsyntenin-1, 1810034E21Rik
MMRRC Submission 040779-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3838 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 149670925-149733356 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 149722790 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 476 (E476G)
Ref Sequence ENSEMBL: ENSMUSP00000101316 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000039144] [ENSMUST00000105691]
AlphaFold Q9EPL2
Predicted Effect possibly damaging
Transcript: ENSMUST00000039144
AA Change: E486G

PolyPhen 2 Score 0.693 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000036962
Gene: ENSMUSG00000039953
AA Change: E486G

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
CA 59 162 1.25e-11 SMART
CA 185 263 1.03e-3 SMART
Pfam:Laminin_G_3 365 510 3.3e-9 PFAM
low complexity region 663 674 N/A INTRINSIC
transmembrane domain 860 882 N/A INTRINSIC
coiled coil region 915 949 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000105691
AA Change: E476G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000101316
Gene: ENSMUSG00000039953
AA Change: E476G

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
CA 59 152 2.91e-12 SMART
CA 175 253 1.03e-3 SMART
Pfam:Laminin_G_3 350 544 1.1e-12 PFAM
low complexity region 653 664 N/A INTRINSIC
transmembrane domain 850 872 N/A INTRINSIC
coiled coil region 905 939 N/A INTRINSIC
Meta Mutation Damage Score 0.2863 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.8%
  • 20x: 96.4%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the calsyntenin family, a subset of the cadherin superfamily. The encoded transmembrane protein, also known as alcadein-alpha, is thought to bind to kinesin-1 motors to mediate the axonal anterograde transport of certain types of vesicle. Amyloid precursor protein (APP) is trafficked via these vesicles and so this protein is being investigated to see how it might contribute to the mechanisms underlying Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
PHENOTYPE: Juvenile mice homozygous for a null allele show reduced basal excitatory synaptic transmission, abnormal excitatory postsynaptic currents, enhanced NMDA receptor-dependent long term potentiation, and delayed dendritic spine maturation in CA1 hippocampal pyramidal cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930486L24Rik A G 13: 60,993,041 (GRCm39) Y213H probably damaging Het
Alg8 C T 7: 97,037,752 (GRCm39) H379Y probably damaging Het
Arhgef25 T C 10: 127,025,605 (GRCm39) T12A probably benign Het
Arid4a A G 12: 71,122,559 (GRCm39) E980G possibly damaging Het
Aspm C T 1: 139,405,792 (GRCm39) H1560Y probably benign Het
Atg10 A T 13: 91,085,499 (GRCm39) I150K probably damaging Het
Bud13 A C 9: 46,201,490 (GRCm39) Q387P possibly damaging Het
Champ1 A G 8: 13,929,939 (GRCm39) Y699C probably damaging Het
Col2a1 T C 15: 97,886,857 (GRCm39) D345G unknown Het
Col2a1 A T 15: 97,898,462 (GRCm39) probably benign Het
Col9a2 C G 4: 120,911,455 (GRCm39) R599G probably damaging Het
Dnajb2 G A 1: 75,218,124 (GRCm39) probably null Het
Dock4 G T 12: 40,844,623 (GRCm39) probably null Het
Epx A T 11: 87,765,656 (GRCm39) L101Q probably damaging Het
F13a1 A T 13: 37,231,398 (GRCm39) N21K probably damaging Het
Fam13c C T 10: 70,378,478 (GRCm39) S336L probably damaging Het
Foxj3 T A 4: 119,473,821 (GRCm39) H215Q possibly damaging Het
Gcnt4 A T 13: 97,083,522 (GRCm39) R273* probably null Het
Gpam T C 19: 55,068,890 (GRCm39) N450S probably benign Het
Hivep2 C A 10: 14,004,713 (GRCm39) T437K probably benign Het
Hmcn2 T C 2: 31,303,419 (GRCm39) L3020P probably damaging Het
Hmgcr A G 13: 96,795,597 (GRCm39) I324T probably benign Het
Ighmbp2 T C 19: 3,321,658 (GRCm39) Y367C probably benign Het
Lrrc14b A G 13: 74,511,664 (GRCm39) C139R possibly damaging Het
Lsamp A T 16: 41,954,675 (GRCm39) E174V possibly damaging Het
Mid1ip1 T C X: 10,584,620 (GRCm39) V51A possibly damaging Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Msn C A X: 95,203,805 (GRCm39) Q303K probably damaging Het
Myh7b A G 2: 155,474,909 (GRCm39) K1816E probably damaging Het
Nap1l1 T A 10: 111,331,183 (GRCm39) probably null Het
Nme2 T A 11: 93,840,803 (GRCm39) E252D probably benign Het
Ntpcr G A 8: 126,464,111 (GRCm39) V79M probably damaging Het
Ogdh C T 11: 6,288,627 (GRCm39) R235* probably null Het
Or10d1 A G 9: 39,484,267 (GRCm39) V96A probably benign Het
Or10w1 A G 19: 13,632,321 (GRCm39) D176G probably benign Het
Or9k2 C A 10: 129,998,275 (GRCm39) E307* probably null Het
P3r3urf A G 4: 116,030,718 (GRCm39) T41A probably benign Het
Pcdh20 T C 14: 88,705,899 (GRCm39) N467S probably benign Het
Pkhd1 G A 1: 20,604,853 (GRCm39) T1154I possibly damaging Het
Polq G T 16: 36,898,711 (GRCm39) R2157I probably damaging Het
Reep6 C A 10: 80,171,723 (GRCm39) A533E probably damaging Het
Senp2 T C 16: 21,828,485 (GRCm39) S32P probably damaging Het
Septin11 T A 5: 93,296,258 (GRCm39) I52N probably damaging Het
Shld2 T C 14: 33,967,325 (GRCm39) D77G probably benign Het
Slc17a4 C T 13: 24,085,752 (GRCm39) R387H probably benign Het
Spdye4b C T 5: 143,178,084 (GRCm39) T11I probably benign Het
Srrt C T 5: 137,300,387 (GRCm39) probably null Het
Sspo T A 6: 48,457,754 (GRCm39) C3085S probably damaging Het
Stim1 C T 7: 102,060,503 (GRCm39) T182I possibly damaging Het
Thbs2 C A 17: 14,908,113 (GRCm39) V217L probably benign Het
Thpo G A 16: 20,547,498 (GRCm39) R38C probably damaging Het
Tmem210 A G 2: 25,178,444 (GRCm39) E35G possibly damaging Het
Trim12c T A 7: 103,990,075 (GRCm39) probably benign Het
Tvp23b A G 11: 62,774,455 (GRCm39) H33R possibly damaging Het
Usp14 A G 18: 10,024,532 (GRCm39) probably null Het
Vmn2r73 A G 7: 85,507,258 (GRCm39) W685R probably benign Het
Zfp618 G A 4: 63,051,801 (GRCm39) A861T probably benign Het
Zfp715 A G 7: 42,949,180 (GRCm39) V260A probably benign Het
Other mutations in Clstn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00486:Clstn1 APN 4 149,719,700 (GRCm39) missense probably damaging 0.99
IGL00585:Clstn1 APN 4 149,722,769 (GRCm39) missense probably benign 0.05
IGL00911:Clstn1 APN 4 149,727,648 (GRCm39) splice site probably benign
IGL01394:Clstn1 APN 4 149,719,239 (GRCm39) missense possibly damaging 0.87
IGL02193:Clstn1 APN 4 149,729,809 (GRCm39) missense probably benign 0.03
IGL02406:Clstn1 APN 4 149,711,816 (GRCm39) missense probably damaging 1.00
IGL02501:Clstn1 APN 4 149,716,299 (GRCm39) missense probably damaging 1.00
IGL02641:Clstn1 APN 4 149,713,968 (GRCm39) missense probably null 1.00
R0012:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0020:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0021:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0026:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0031:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0038:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0062:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0064:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0193:Clstn1 UTSW 4 149,719,253 (GRCm39) missense probably damaging 0.96
R0279:Clstn1 UTSW 4 149,728,131 (GRCm39) missense probably damaging 1.00
R0394:Clstn1 UTSW 4 149,728,635 (GRCm39) missense probably benign 0.00
R0609:Clstn1 UTSW 4 149,713,757 (GRCm39) splice site probably null
R0685:Clstn1 UTSW 4 149,731,312 (GRCm39) missense probably benign 0.24
R0724:Clstn1 UTSW 4 149,728,081 (GRCm39) missense possibly damaging 0.84
R1016:Clstn1 UTSW 4 149,731,286 (GRCm39) missense probably benign 0.21
R1470:Clstn1 UTSW 4 149,719,179 (GRCm39) missense possibly damaging 0.94
R1470:Clstn1 UTSW 4 149,719,179 (GRCm39) missense possibly damaging 0.94
R1622:Clstn1 UTSW 4 149,713,864 (GRCm39) missense probably damaging 0.97
R1680:Clstn1 UTSW 4 149,728,183 (GRCm39) missense probably benign 0.02
R3803:Clstn1 UTSW 4 149,719,796 (GRCm39) missense probably damaging 0.99
R3836:Clstn1 UTSW 4 149,722,790 (GRCm39) missense probably damaging 1.00
R4923:Clstn1 UTSW 4 149,729,486 (GRCm39) missense probably benign 0.07
R5024:Clstn1 UTSW 4 149,719,751 (GRCm39) missense possibly damaging 0.91
R5919:Clstn1 UTSW 4 149,719,703 (GRCm39) missense probably damaging 1.00
R6269:Clstn1 UTSW 4 149,728,524 (GRCm39) missense probably benign 0.00
R6354:Clstn1 UTSW 4 149,727,673 (GRCm39) missense probably benign 0.05
R6382:Clstn1 UTSW 4 149,710,577 (GRCm39) splice site probably null
R6573:Clstn1 UTSW 4 149,728,146 (GRCm39) missense probably damaging 1.00
R7342:Clstn1 UTSW 4 149,713,887 (GRCm39) missense probably damaging 0.98
R7457:Clstn1 UTSW 4 149,719,373 (GRCm39) missense probably benign 0.03
R7571:Clstn1 UTSW 4 149,730,744 (GRCm39) missense probably benign 0.38
R7682:Clstn1 UTSW 4 149,710,558 (GRCm39) missense possibly damaging 0.72
R7738:Clstn1 UTSW 4 149,719,811 (GRCm39) missense probably damaging 1.00
R7803:Clstn1 UTSW 4 149,716,328 (GRCm39) missense probably damaging 1.00
R7904:Clstn1 UTSW 4 149,698,594 (GRCm39) missense probably benign 0.01
R7918:Clstn1 UTSW 4 149,728,508 (GRCm39) missense probably damaging 0.98
R8007:Clstn1 UTSW 4 149,716,305 (GRCm39) missense probably damaging 1.00
R8821:Clstn1 UTSW 4 149,730,780 (GRCm39) missense probably benign 0.00
R8831:Clstn1 UTSW 4 149,730,780 (GRCm39) missense probably benign 0.00
R9169:Clstn1 UTSW 4 149,731,322 (GRCm39) missense possibly damaging 0.68
R9173:Clstn1 UTSW 4 149,710,564 (GRCm39) missense probably benign 0.08
R9463:Clstn1 UTSW 4 149,698,564 (GRCm39) missense possibly damaging 0.92
R9491:Clstn1 UTSW 4 149,731,929 (GRCm39) missense probably damaging 1.00
R9615:Clstn1 UTSW 4 149,722,757 (GRCm39) missense probably damaging 1.00
X0020:Clstn1 UTSW 4 149,719,708 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GAAGTCATTCCTACGCGTGAC -3'
(R):5'- AATCGATGACATGACTAGTGTTCC -3'

Sequencing Primer
(F):5'- ACGCGTGACTCATCTTCTGGG -3'
(R):5'- GACTAGTGTTCCCTAAAAGGCTACG -3'
Posted On 2015-04-06