Incidental Mutation 'R1016:Clstn1'
ID 96283
Institutional Source Beutler Lab
Gene Symbol Clstn1
Ensembl Gene ENSMUSG00000039953
Gene Name calsyntenin 1
Synonyms Cst-1, alcadein alpha, calsyntenin-1, 1810034E21Rik
MMRRC Submission 039120-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1016 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 149670925-149733356 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 149731286 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 866 (I866T)
Ref Sequence ENSEMBL: ENSMUSP00000101316 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038859] [ENSMUST00000039144] [ENSMUST00000105688] [ENSMUST00000105689] [ENSMUST00000105690] [ENSMUST00000105691] [ENSMUST00000122059] [ENSMUST00000177654] [ENSMUST00000118704]
AlphaFold Q9EPL2
Predicted Effect probably benign
Transcript: ENSMUST00000038859
SMART Domains Protein: ENSMUSP00000036434
Gene: ENSMUSG00000039936

DomainStartEndE-ValueType
PI3K_p85B 31 108 2.24e-26 SMART
PI3K_rbd 174 281 1.3e-13 SMART
PI3K_C2 309 412 1.87e-28 SMART
PI3Ka 496 685 8.56e-87 SMART
PI3Kc 776 1042 5.65e-128 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000039144
AA Change: I876T

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000036962
Gene: ENSMUSG00000039953
AA Change: I876T

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 benign
Transcript: ENSMUST00000105688
SMART Domains Protein: ENSMUSP00000101313
Gene: ENSMUSG00000039936

DomainStartEndE-ValueType
PI3K_p85B 31 108 2.24e-26 SMART
PI3K_rbd 174 281 1.3e-13 SMART
PI3K_C2 309 412 1.87e-28 SMART
PI3Ka 496 685 8.56e-87 SMART
PI3Kc 775 1041 5.65e-128 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000105689
SMART Domains Protein: ENSMUSP00000101314
Gene: ENSMUSG00000039936

DomainStartEndE-ValueType
PI3K_p85B 31 108 2.24e-26 SMART
PI3K_rbd 174 281 1.3e-13 SMART
PI3K_C2 309 412 1.87e-28 SMART
PI3Ka 496 684 1.35e-84 SMART
PI3Kc 774 1040 5.65e-128 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000105690
SMART Domains Protein: ENSMUSP00000101315
Gene: ENSMUSG00000039936

DomainStartEndE-ValueType
PI3K_p85B 31 108 2.24e-26 SMART
PI3K_rbd 174 281 1.3e-13 SMART
PI3K_C2 309 412 1.87e-28 SMART
PI3Ka 496 688 1.22e-82 SMART
PI3Kc 778 1044 5.65e-128 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000105691
AA Change: I866T

PolyPhen 2 Score 0.207 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000101316
Gene: ENSMUSG00000039953
AA Change: I866T

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
Predicted Effect probably benign
Transcript: ENSMUST00000122059
SMART Domains Protein: ENSMUSP00000113844
Gene: ENSMUSG00000039936

DomainStartEndE-ValueType
PI3K_p85B 31 108 2.24e-26 SMART
PI3K_rbd 174 281 1.3e-13 SMART
PI3K_C2 309 408 6.47e-23 SMART
PI3Ka 492 681 8.56e-87 SMART
PI3Kc 771 1037 5.65e-128 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000177654
SMART Domains Protein: ENSMUSP00000136045
Gene: ENSMUSG00000039936

DomainStartEndE-ValueType
PI3K_p85B 31 108 2.24e-26 SMART
PI3K_rbd 174 281 1.3e-13 SMART
PI3K_C2 309 412 1.87e-28 SMART
PI3Ka 496 688 1.22e-82 SMART
PI3Kc 778 1044 5.65e-128 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000118704
SMART Domains Protein: ENSMUSP00000112863
Gene: ENSMUSG00000039936

DomainStartEndE-ValueType
PI3K_p85B 31 108 2.24e-26 SMART
PI3K_rbd 174 281 1.3e-13 SMART
PI3K_C2 309 412 1.87e-28 SMART
PI3Ka 496 687 1.8e-80 SMART
PI3Kc 777 1043 5.65e-128 SMART
Coding Region Coverage
  • 1x: 98.7%
  • 3x: 97.5%
  • 10x: 93.6%
  • 20x: 84.3%
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: 31 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ceacam20 T A 7: 19,710,227 (GRCm39) H6Q probably null Het
Cntnap1 T C 11: 101,068,333 (GRCm39) V86A probably damaging Het
Crtc1 A T 8: 70,844,769 (GRCm39) Y351* probably null Het
Cul7 T A 17: 46,974,116 (GRCm39) L1467H probably damaging Het
Cyp2j12 C T 4: 96,001,102 (GRCm39) probably null Het
Dmrt2 A T 19: 25,652,938 (GRCm39) K183N probably damaging Het
Fancl G T 11: 26,337,195 (GRCm39) probably benign Het
Fbxo40 G A 16: 36,789,539 (GRCm39) Q524* probably null Het
Flcn T C 11: 59,686,691 (GRCm39) probably null Het
Gm19965 T A 1: 116,749,031 (GRCm39) C237* probably null Het
Hpf1 A G 8: 61,348,678 (GRCm39) Y131C possibly damaging Het
Mdh1 A G 11: 21,509,769 (GRCm39) L202P probably benign Het
Mpl T C 4: 118,306,110 (GRCm39) Y310C probably damaging Het
Mtus1 A G 8: 41,503,063 (GRCm39) V784A probably benign Het
Myg1 T C 15: 102,242,786 (GRCm39) I159T possibly damaging Het
Nans T C 4: 46,500,716 (GRCm39) Y203H probably benign Het
Ncapg2 G A 12: 116,402,295 (GRCm39) C709Y probably damaging Het
Or8b36 T C 9: 37,937,987 (GRCm39) V295A probably damaging Het
Parp12 T C 6: 39,088,660 (GRCm39) Y192C probably damaging Het
Plekha6 A G 1: 133,187,832 (GRCm39) N118D probably benign Het
Prg4 T C 1: 150,330,442 (GRCm39) probably benign Het
Psip1 T C 4: 83,378,135 (GRCm39) T454A possibly damaging Het
Ptprz1 T C 6: 23,000,973 (GRCm39) L1021P probably damaging Het
Pvr T C 7: 19,643,142 (GRCm39) I364V probably benign Het
Serpina5 A G 12: 104,071,582 (GRCm39) I396M probably damaging Het
Sgcb A C 5: 73,797,183 (GRCm39) H192Q probably benign Het
Slc4a9 C A 18: 36,664,478 (GRCm39) H379N probably benign Het
Tet1 T C 10: 62,715,729 (GRCm39) D22G probably benign Het
Trim34a T C 7: 103,897,167 (GRCm39) V77A probably benign Het
Ttc7b T C 12: 100,369,617 (GRCm39) E384G probably null Het
Vmn2r16 G A 5: 109,487,754 (GRCm39) G209D probably damaging 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
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
R3838: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'- GTCACTTACACAAGGAAGCTCGCTC -3'
(R):5'- AGTTGCCTGCCTATGCTACTCACG -3'

Sequencing Primer
(F):5'- GAAGCACTCTGACACATTCCATTTG -3'
(R):5'- AAGGGCTTCCTCATCTGAAGG -3'
Posted On 2014-01-05