Incidental Mutation 'R0724:Clstn1'
ID 262004
Institutional Source Beutler Lab
Gene Symbol Clstn1
Ensembl Gene ENSMUSG00000039953
Gene Name calsyntenin 1
Synonyms Cst-1, alcadein alpha, calsyntenin-1, 1810034E21Rik
MMRRC Submission 038906-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0724 (G1)
Quality Score 23
Status Validated
Chromosome 4
Chromosomal Location 149670925-149733356 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 149728081 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Alanine at position 583 (D583A)
Ref Sequence ENSEMBL: ENSMUSP00000101316 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000039144] [ENSMUST00000105691]
AlphaFold Q9EPL2
Predicted Effect probably benign
Transcript: ENSMUST00000039144
AA Change: D593A

PolyPhen 2 Score 0.187 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000036962
Gene: ENSMUSG00000039953
AA Change: D593A

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 possibly damaging
Transcript: ENSMUST00000105691
AA Change: D583A

PolyPhen 2 Score 0.841 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000101316
Gene: ENSMUSG00000039953
AA Change: D583A

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 0.1795 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.9%
  • 10x: 97.5%
  • 20x: 95.2%
Validation Efficiency 100% (62/62)
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700018F24Rik A G 5: 144,981,573 (GRCm39) E136G probably benign Het
Adgre4 T A 17: 56,159,281 (GRCm39) S655R probably benign Het
Ak7 T A 12: 105,676,513 (GRCm39) V71E probably benign Het
Ank2 C T 3: 126,755,986 (GRCm39) R1077H probably damaging Het
Anxa3 A G 5: 96,976,607 (GRCm39) T198A possibly damaging Het
Atp1a1 A T 3: 101,499,755 (GRCm39) I109N possibly damaging Het
Camta1 A G 4: 151,162,349 (GRCm39) I119T probably damaging Het
Carm1 A G 9: 21,498,670 (GRCm39) Y504C probably damaging Het
Casp1 C T 9: 5,303,077 (GRCm39) P177L probably benign Het
Ccdc122 C A 14: 77,329,517 (GRCm39) probably benign Het
Ces1a A G 8: 93,766,141 (GRCm39) S158P probably damaging Het
Ces3a T A 8: 105,776,827 (GRCm39) D103E possibly damaging Het
Corin A G 5: 72,490,138 (GRCm39) probably benign Het
Cryba1 T C 11: 77,610,283 (GRCm39) D144G probably damaging Het
Cwf19l2 G T 9: 3,421,377 (GRCm39) probably null Het
Dis3l T C 9: 64,214,408 (GRCm39) T1027A possibly damaging Het
Dop1b A G 16: 93,559,213 (GRCm39) E653G probably benign Het
Dst A G 1: 34,227,758 (GRCm39) I1459V probably benign Het
Dyrk3 T C 1: 131,057,877 (GRCm39) T64A probably benign Het
Emp2 C T 16: 10,102,479 (GRCm39) C111Y probably benign Het
Enam A G 5: 88,649,853 (GRCm39) Y454C probably damaging Het
Fbn1 A T 2: 125,193,984 (GRCm39) C1328S probably benign Het
Gata3 T C 2: 9,879,386 (GRCm39) T197A probably benign Het
Gm1043 A G 5: 37,344,573 (GRCm39) T212A probably damaging Het
H2-Eb1 T C 17: 34,534,006 (GRCm39) probably benign Het
Hand1 T C 11: 57,722,506 (GRCm39) H36R probably damaging Het
Hmgcs2 C A 3: 98,204,317 (GRCm39) Y239* probably null Het
Hoxc12 A G 15: 102,845,490 (GRCm39) Y68C probably damaging Het
Inpp5a A G 7: 139,096,579 (GRCm39) I143V probably benign Het
Klhdc2 C A 12: 69,343,822 (GRCm39) F18L probably benign Het
Kpnb1 T C 11: 97,069,130 (GRCm39) Y251C probably damaging Het
Lrch4 A T 5: 137,635,570 (GRCm39) N315I probably damaging Het
Map3k10 A C 7: 27,367,780 (GRCm39) V286G probably damaging Het
Myo7b G A 18: 32,138,602 (GRCm39) probably benign Het
Nlrp2 G T 7: 5,322,221 (GRCm39) L809I probably damaging Het
Oacyl T C 18: 65,870,896 (GRCm39) probably benign Het
Or4q3 A G 14: 50,583,374 (GRCm39) V175A possibly damaging Het
Paxbp1 T A 16: 90,833,424 (GRCm39) D270V probably damaging Het
Pdia3 G A 2: 121,262,858 (GRCm39) G275S probably damaging Het
Pira13 T C 7: 3,819,871 (GRCm39) N564S possibly damaging Het
Plcb3 G A 19: 6,940,760 (GRCm39) R359C probably damaging Het
Plcxd3 G A 15: 4,546,350 (GRCm39) S118N probably damaging Het
Ptpn14 T C 1: 189,583,144 (GRCm39) S664P possibly damaging Het
Sirt1 T C 10: 63,159,752 (GRCm39) I443V possibly damaging Het
Slc7a8 G A 14: 54,972,643 (GRCm39) probably benign Het
Smim14 A G 5: 65,610,682 (GRCm39) probably benign Het
Sost C T 11: 101,857,744 (GRCm39) C19Y probably benign Het
Tcaf1 G T 6: 42,652,301 (GRCm39) A727E probably damaging Het
Thoc1 T C 18: 9,963,829 (GRCm39) L144P probably damaging Het
Tmem132b A T 5: 125,860,485 (GRCm39) T577S possibly damaging Het
Tnfrsf21 C T 17: 43,349,104 (GRCm39) H239Y probably benign Het
Tshr T C 12: 91,505,060 (GRCm39) F666S probably damaging Het
Wdr1 A G 5: 38,698,205 (GRCm39) V192A possibly damaging Het
Zfp697 T C 3: 98,335,482 (GRCm39) W416R 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
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
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'- AGGTCCCTGAAGATGCCAACAGAG -3'
(R):5'- AGATCAAGTGATGACCCACCTTCCC -3'

Sequencing Primer
(F):5'- GGACTTTACCCTATGTGAGCATC -3'
(R):5'- AACAGGCTAAAGACCTAAAGGC -3'
Posted On 2015-02-04