Incidental Mutation 'R8821:Clstn1'
ID 673035
Institutional Source Beutler Lab
Gene Symbol Clstn1
Ensembl Gene ENSMUSG00000039953
Gene Name calsyntenin 1
Synonyms Cst-1, alcadein alpha, calsyntenin-1, 1810034E21Rik
MMRRC Submission 068654-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R8821 (G1)
Quality Score 225.009
Status Validated
Chromosome 4
Chromosomal Location 149670925-149733356 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 149730780 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glutamine at position 837 (R837Q)
Ref Sequence ENSEMBL: ENSMUSP00000036962 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038859] [ENSMUST00000039144] [ENSMUST00000105688] [ENSMUST00000105689] [ENSMUST00000105690] [ENSMUST00000105691] [ENSMUST00000118704] [ENSMUST00000122059] [ENSMUST00000177654]
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: R837Q

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000036962
Gene: ENSMUSG00000039953
AA Change: R837Q

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: R827Q

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000101316
Gene: ENSMUSG00000039953
AA Change: R827Q

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: 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
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
Meta Mutation Damage Score 0.0846 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (74/74)
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A230072I06Rik A T 8: 12,329,688 (GRCm39) I48L unknown Het
Abca8a A T 11: 109,949,362 (GRCm39) I927K probably damaging Het
Abcc3 A C 11: 94,241,787 (GRCm39) C1415G probably damaging Het
Abcf3 C T 16: 20,369,214 (GRCm39) R205C probably damaging Het
Aldh3a1 A G 11: 61,107,142 (GRCm39) Y282C probably damaging Het
Alyref CCCGCGCGGCGGCCTGCACTGCGCCGCCGCGGCCGCCCTGGGAGCCGGCCCTGCCGCG CCCGCG 11: 120,489,023 (GRCm39) probably null Het
Arfgef3 A G 10: 18,528,491 (GRCm39) S299P possibly damaging Het
Asic2 A T 11: 81,858,726 (GRCm39) N95K probably damaging Het
Atp2c2 A G 8: 120,476,033 (GRCm39) probably null Het
Btbd18 A G 2: 84,497,601 (GRCm39) D413G probably damaging Het
C8b A G 4: 104,647,874 (GRCm39) Y355C probably damaging Het
Carm1 A G 9: 21,491,663 (GRCm39) E244G probably damaging Het
Castor2 T A 5: 134,164,092 (GRCm39) V96E possibly damaging Het
Catsperg1 A T 7: 28,904,361 (GRCm39) probably benign Het
Cish T A 9: 107,177,671 (GRCm39) F116I probably damaging Het
Ckmt1 G A 2: 121,191,302 (GRCm39) probably benign Het
Clasrp C T 7: 19,320,362 (GRCm39) R432H unknown Het
Col27a1 A G 4: 63,143,148 (GRCm39) T279A probably benign Het
Cox10 A G 11: 63,855,306 (GRCm39) F325S probably damaging Het
Cpne5 T C 17: 29,430,668 (GRCm39) I81V probably benign Het
Ctps1 A T 4: 120,424,507 (GRCm39) S36T possibly damaging Het
Dchs2 T C 3: 83,192,670 (GRCm39) L1705P probably benign Het
Dcstamp A G 15: 39,618,185 (GRCm39) H198R probably benign Het
Dhx58 T A 11: 100,594,806 (GRCm39) K30M probably damaging Het
Dnah1 C T 14: 31,018,455 (GRCm39) A1392T probably benign Het
Dnah14 C A 1: 181,619,569 (GRCm39) Y3964* probably null Het
Dnah8 T C 17: 31,013,712 (GRCm39) S3818P probably damaging Het
Dnmt3b T A 2: 153,518,734 (GRCm39) N632K probably benign Het
Drc7 G A 8: 95,788,845 (GRCm39) R301Q probably damaging Het
Dsg1a T C 18: 20,453,365 (GRCm39) V21A probably damaging Het
Dtd1 T C 2: 144,459,261 (GRCm39) L95P probably benign Het
Efhb A T 17: 53,707,772 (GRCm39) probably benign Het
Fam186b T A 15: 99,178,733 (GRCm39) M198L possibly damaging Het
Fam193a A G 5: 34,616,374 (GRCm39) T850A probably benign Het
Fan1 G A 7: 64,004,249 (GRCm39) P739L probably damaging Het
Flii A T 11: 60,616,074 (GRCm39) N28K probably benign Het
Fmo3 T C 1: 162,796,407 (GRCm39) Y55C probably damaging Het
Gfi1 G A 5: 107,868,138 (GRCm39) R377C probably damaging Het
Gm9195 C T 14: 72,717,536 (GRCm39) E266K possibly damaging Het
Hdac1-ps T A 17: 78,799,969 (GRCm39) L320Q probably damaging Het
Helz A T 11: 107,525,919 (GRCm39) M825L probably damaging Het
Hsd3b9 A T 3: 98,354,047 (GRCm39) W151R probably benign Het
Ift80 G A 3: 68,869,583 (GRCm39) A236V probably damaging Het
Il1rn A T 2: 24,239,505 (GRCm39) T134S possibly damaging Het
Imp4 T C 1: 34,483,445 (GRCm39) M257T probably benign Het
Impdh2 T C 9: 108,441,957 (GRCm39) L377S probably damaging Het
Kcnrg T C 14: 61,844,981 (GRCm39) V7A possibly damaging Het
Kdm1b C A 13: 47,217,617 (GRCm39) L359I possibly damaging Het
Lima1 T A 15: 99,704,306 (GRCm39) T288S probably benign Het
Lrrc37 A T 11: 103,510,470 (GRCm39) D499E unknown Het
Lrrc4c A T 2: 97,460,040 (GRCm39) D222V possibly damaging Het
Mybpc3 T A 2: 90,948,524 (GRCm39) V4E probably null Het
Ncor1 A T 11: 62,260,234 (GRCm39) D505E probably benign Het
Nell1 A G 7: 50,476,097 (GRCm39) S579G probably damaging Het
Npc1 T A 18: 12,333,877 (GRCm39) M735L probably benign Het
Or1j13 G A 2: 36,369,794 (GRCm39) T116I possibly damaging Het
Or2at4 A G 7: 99,384,893 (GRCm39) H181R possibly damaging Het
Or4a73 A G 2: 89,420,880 (GRCm39) I193T probably damaging Het
Pcdhb12 A G 18: 37,570,386 (GRCm39) M511V probably benign Het
Peli2 G A 14: 48,490,130 (GRCm39) E201K possibly damaging Het
Phf3 T A 1: 30,860,347 (GRCm39) K828* probably null Het
Pih1d1 A G 7: 44,806,196 (GRCm39) D44G possibly damaging Het
Prag1 A T 8: 36,613,891 (GRCm39) T1148S probably benign Het
Ptpn18 A T 1: 34,511,271 (GRCm39) R338W probably null Het
Slc7a6os A T 8: 106,937,189 (GRCm39) D90E probably benign Het
Sp7 T A 15: 102,267,227 (GRCm39) H211L possibly damaging Het
Ssh3 A G 19: 4,319,053 (GRCm39) V19A possibly damaging Het
Tcp11l2 A G 10: 84,449,522 (GRCm39) I496V probably damaging Het
Tenm3 C T 8: 48,729,417 (GRCm39) A1530T Het
Tmem232 A G 17: 65,743,367 (GRCm39) L308P probably damaging Het
Tulp4 A G 17: 6,189,409 (GRCm39) N77S probably damaging Het
Unc13d AATGCCTCCCATGCC AATGCCTCCCATGCCTCCCATGCC 11: 115,958,998 (GRCm39) probably benign Het
Usp48 A T 4: 137,341,080 (GRCm39) D360V probably damaging Het
Vmn2r84 G A 10: 130,226,968 (GRCm39) A290V probably benign Het
Zfp1007 A T 5: 109,824,174 (GRCm39) S425R probably benign Het
Zfp512b T C 2: 181,228,525 (GRCm39) N738S 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
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
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'- ACACTGTCACACTGTTGTAAAC -3'
(R):5'- TGTGAGCTACGCTTGCTACC -3'

Sequencing Primer
(F):5'- GGTCACTGTTTGCCCCCAG -3'
(R):5'- ACGCTTGCTACCAGGTTTG -3'
Posted On 2021-04-30