Incidental Mutation 'R8047:Clstn3'
ID 618812
Institutional Source Beutler Lab
Gene Symbol Clstn3
Ensembl Gene ENSMUSG00000008153
Gene Name calsyntenin 3
Synonyms Cst-3, CSTN3, alcadein-beta
MMRRC Submission 067484-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R8047 (G1)
Quality Score 225.009
Status Not validated
Chromosome 6
Chromosomal Location 124407715-124441743 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 124408972 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 892 (D892V)
Ref Sequence ENSEMBL: ENSMUSP00000008297 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000008297] [ENSMUST00000112523]
AlphaFold Q99JH7
Predicted Effect possibly damaging
Transcript: ENSMUST00000008297
AA Change: D892V

PolyPhen 2 Score 0.730 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000008297
Gene: ENSMUSG00000008153
AA Change: D892V

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
CA 50 143 2.72e-12 SMART
CA 166 244 4.04e-2 SMART
SCOP:d1a8d_1 333 549 7e-23 SMART
transmembrane domain 846 868 N/A INTRINSIC
low complexity region 928 945 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000112523
AA Change: D855V

PolyPhen 2 Score 0.730 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000108142
Gene: ENSMUSG00000008153
AA Change: D855V

DomainStartEndE-ValueType
CA 13 106 2.72e-12 SMART
CA 129 207 4.04e-2 SMART
Pfam:Laminin_G_3 304 505 4.1e-8 PFAM
transmembrane domain 809 831 N/A INTRINSIC
low complexity region 891 908 N/A INTRINSIC
Meta Mutation Damage Score 0.0998 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency
MGI Phenotype PHENOTYPE: Mice homozygous for a knock-out allele exhibit reductions in excitatory and inhibitory synapse density and deficits in synaptic transmission. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abce1 G A 8: 80,427,817 (GRCm39) T157I possibly damaging Het
Cd200l2 T C 16: 45,340,829 (GRCm39) I245V probably benign Het
Cdh22 G A 2: 165,012,687 (GRCm39) R133W probably damaging Het
Cep152 A T 2: 125,406,247 (GRCm39) N1428K probably benign Het
Coch G A 12: 51,650,496 (GRCm39) probably null Het
D6Ertd527e G T 6: 87,088,454 (GRCm39) V206F unknown Het
Dnaaf9 A T 2: 130,617,019 (GRCm39) V439E probably damaging Het
Dock3 T C 9: 106,870,208 (GRCm39) I625M possibly damaging Het
Dpy19l4 A G 4: 11,317,139 (GRCm39) S20P probably benign Het
Eef1e1 T C 13: 38,830,222 (GRCm39) Q150R probably damaging Het
Eln CTCCAGCTCCGAT C 5: 134,758,003 (GRCm39) probably benign Het
Engase T C 11: 118,377,282 (GRCm39) S526P probably benign Het
Fbxo40 T A 16: 36,790,231 (GRCm39) D293V probably damaging Het
Gipc3 T A 10: 81,177,132 (GRCm39) N146I probably damaging Het
Gm11569 T C 11: 99,689,616 (GRCm39) T28A unknown Het
Gm43302 T C 5: 105,422,623 (GRCm39) I470V possibly damaging Het
Gpihbp1 A G 15: 75,469,627 (GRCm39) Q114R possibly damaging Het
Grhl2 T A 15: 37,336,465 (GRCm39) M454K probably benign Het
Gsap A T 5: 21,462,866 (GRCm39) probably null Het
Ighv6-5 T C 12: 114,380,191 (GRCm39) probably null Het
Kif1b C A 4: 149,299,379 (GRCm39) V1010L probably damaging Het
Krt8 A T 15: 101,912,406 (GRCm39) I90N probably damaging Het
Lrrc69 A T 4: 14,773,726 (GRCm39) I110N probably benign Het
Lta T C 17: 35,423,011 (GRCm39) Y104C probably damaging Het
Madd A G 2: 91,009,546 (GRCm39) Y13H probably damaging Het
Mccc2 C T 13: 100,091,181 (GRCm39) V439I probably benign Het
Mecom T A 3: 30,292,404 (GRCm39) D35V Het
Msra C T 14: 64,522,612 (GRCm39) A76T probably damaging Het
Myo18b G T 5: 112,871,681 (GRCm39) D2133E possibly damaging Het
Ncapd2 C T 6: 125,166,762 (GRCm39) V31M probably damaging Het
Npc1 A G 18: 12,346,374 (GRCm39) V274A probably benign Het
Or5m11b T C 2: 85,806,271 (GRCm39) I228T possibly damaging Het
Patz1 C T 11: 3,256,283 (GRCm39) P523L probably benign Het
Pbx2 T C 17: 34,814,262 (GRCm39) S350P probably benign Het
Plk4 T C 3: 40,760,187 (GRCm39) I361T probably benign Het
Ppat G T 5: 77,073,557 (GRCm39) N122K probably damaging Het
Prss23 T A 7: 89,159,136 (GRCm39) Q311L probably damaging Het
Psg26 G T 7: 18,212,474 (GRCm39) Q294K possibly damaging Het
Rab3il1 G T 19: 10,011,166 (GRCm39) R285L probably benign Het
Radil A G 5: 142,480,695 (GRCm39) C587R probably damaging Het
Rd3 A T 1: 191,709,620 (GRCm39) probably benign Het
Reck T C 4: 43,927,221 (GRCm39) L504P probably damaging Het
Rmc1 C T 18: 12,313,586 (GRCm39) T233M possibly damaging Het
Selenov A C 7: 27,990,108 (GRCm39) L132R probably benign Het
Spag16 A T 1: 69,882,155 (GRCm39) D49V probably damaging Het
Ston2 C T 12: 91,608,617 (GRCm39) V828I probably damaging Het
Tiam1 A G 16: 89,694,672 (GRCm39) S262P probably benign Het
Tlnrd1 A T 7: 83,532,069 (GRCm39) S121T probably damaging Het
Unc13c T A 9: 73,719,636 (GRCm39) K1011* probably null Het
Vmn2r89 T A 14: 51,692,549 (GRCm39) D117E probably benign Het
Zbtb7c A C 18: 76,270,221 (GRCm39) N103T probably damaging Het
Zfp764 T C 7: 127,005,412 (GRCm39) E75G probably damaging Het
Other mutations in Clstn3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01068:Clstn3 APN 6 124,439,098 (GRCm39) missense probably damaging 1.00
IGL01415:Clstn3 APN 6 124,415,781 (GRCm39) nonsense probably null
IGL01521:Clstn3 APN 6 124,434,990 (GRCm39) nonsense probably null
IGL01537:Clstn3 APN 6 124,408,559 (GRCm39) missense possibly damaging 0.91
IGL01729:Clstn3 APN 6 124,426,753 (GRCm39) missense probably benign 0.06
IGL01879:Clstn3 APN 6 124,415,769 (GRCm39) missense probably damaging 1.00
IGL01998:Clstn3 APN 6 124,435,622 (GRCm39) missense probably damaging 1.00
IGL03130:Clstn3 APN 6 124,436,222 (GRCm39) missense probably damaging 0.98
IGL03405:Clstn3 APN 6 124,415,327 (GRCm39) missense possibly damaging 0.95
PIT4403001:Clstn3 UTSW 6 124,434,982 (GRCm39) missense probably damaging 1.00
R0049:Clstn3 UTSW 6 124,436,812 (GRCm39) missense possibly damaging 0.87
R0049:Clstn3 UTSW 6 124,436,812 (GRCm39) missense possibly damaging 0.87
R0208:Clstn3 UTSW 6 124,409,128 (GRCm39) splice site probably benign
R0276:Clstn3 UTSW 6 124,408,699 (GRCm39) splice site probably benign
R0440:Clstn3 UTSW 6 124,428,372 (GRCm39) missense probably damaging 1.00
R0612:Clstn3 UTSW 6 124,426,459 (GRCm39) missense probably damaging 0.98
R1200:Clstn3 UTSW 6 124,436,129 (GRCm39) missense probably damaging 1.00
R1224:Clstn3 UTSW 6 124,434,878 (GRCm39) missense probably benign
R1378:Clstn3 UTSW 6 124,415,378 (GRCm39) missense probably damaging 1.00
R1491:Clstn3 UTSW 6 124,414,449 (GRCm39) missense possibly damaging 0.51
R1495:Clstn3 UTSW 6 124,426,876 (GRCm39) missense probably benign 0.00
R1511:Clstn3 UTSW 6 124,439,128 (GRCm39) missense probably damaging 1.00
R1655:Clstn3 UTSW 6 124,414,386 (GRCm39) missense probably damaging 1.00
R1731:Clstn3 UTSW 6 124,408,591 (GRCm39) missense probably benign 0.04
R1734:Clstn3 UTSW 6 124,413,773 (GRCm39) splice site probably benign
R1751:Clstn3 UTSW 6 124,408,958 (GRCm39) missense probably damaging 1.00
R1954:Clstn3 UTSW 6 124,436,257 (GRCm39) missense possibly damaging 0.94
R2133:Clstn3 UTSW 6 124,426,462 (GRCm39) missense probably benign
R2192:Clstn3 UTSW 6 124,436,166 (GRCm39) missense probably damaging 1.00
R2314:Clstn3 UTSW 6 124,427,676 (GRCm39) missense probably benign 0.39
R2874:Clstn3 UTSW 6 124,415,294 (GRCm39) missense probably damaging 1.00
R3500:Clstn3 UTSW 6 124,408,670 (GRCm39) missense probably benign 0.01
R3761:Clstn3 UTSW 6 124,434,835 (GRCm39) missense possibly damaging 0.54
R3878:Clstn3 UTSW 6 124,434,901 (GRCm39) missense probably damaging 0.97
R3927:Clstn3 UTSW 6 124,428,327 (GRCm39) missense probably damaging 1.00
R3934:Clstn3 UTSW 6 124,434,901 (GRCm39) missense probably damaging 0.97
R3935:Clstn3 UTSW 6 124,434,901 (GRCm39) missense probably damaging 0.97
R4063:Clstn3 UTSW 6 124,426,792 (GRCm39) missense possibly damaging 0.51
R4402:Clstn3 UTSW 6 124,433,939 (GRCm39) missense probably damaging 0.96
R4534:Clstn3 UTSW 6 124,436,179 (GRCm39) missense probably damaging 1.00
R4785:Clstn3 UTSW 6 124,414,331 (GRCm39) splice site probably null
R4834:Clstn3 UTSW 6 124,408,912 (GRCm39) splice site probably null
R5921:Clstn3 UTSW 6 124,408,539 (GRCm39) utr 3 prime probably benign
R5932:Clstn3 UTSW 6 124,415,291 (GRCm39) missense probably benign 0.01
R6025:Clstn3 UTSW 6 124,408,623 (GRCm39) missense possibly damaging 0.73
R6101:Clstn3 UTSW 6 124,438,629 (GRCm39) missense probably damaging 1.00
R6360:Clstn3 UTSW 6 124,415,388 (GRCm39) missense possibly damaging 0.88
R6578:Clstn3 UTSW 6 124,427,663 (GRCm39) critical splice donor site probably null
R6813:Clstn3 UTSW 6 124,413,894 (GRCm39) missense probably benign 0.00
R7380:Clstn3 UTSW 6 124,433,948 (GRCm39) missense probably benign 0.01
R7419:Clstn3 UTSW 6 124,435,088 (GRCm39) missense probably benign 0.05
R7625:Clstn3 UTSW 6 124,414,377 (GRCm39) nonsense probably null
R7780:Clstn3 UTSW 6 124,439,161 (GRCm39) missense probably damaging 0.98
R7936:Clstn3 UTSW 6 124,408,972 (GRCm39) missense possibly damaging 0.73
R7939:Clstn3 UTSW 6 124,439,158 (GRCm39) missense probably damaging 1.00
R8079:Clstn3 UTSW 6 124,436,763 (GRCm39) missense probably damaging 1.00
R8085:Clstn3 UTSW 6 124,435,683 (GRCm39) missense probably benign 0.23
R8299:Clstn3 UTSW 6 124,414,332 (GRCm39) critical splice donor site probably null
R8406:Clstn3 UTSW 6 124,439,136 (GRCm39) missense probably damaging 1.00
R8685:Clstn3 UTSW 6 124,433,867 (GRCm39) missense probably damaging 1.00
R9045:Clstn3 UTSW 6 124,408,921 (GRCm39) missense probably damaging 0.98
R9209:Clstn3 UTSW 6 124,408,571 (GRCm39) missense probably benign 0.02
R9264:Clstn3 UTSW 6 124,436,727 (GRCm39) missense probably damaging 1.00
R9268:Clstn3 UTSW 6 124,433,880 (GRCm39) missense probably damaging 0.99
R9443:Clstn3 UTSW 6 124,428,358 (GRCm39) missense probably damaging 1.00
RF014:Clstn3 UTSW 6 124,436,225 (GRCm39) nonsense probably null
X0066:Clstn3 UTSW 6 124,426,770 (GRCm39) missense probably benign 0.13
Z1176:Clstn3 UTSW 6 124,436,159 (GRCm39) missense probably damaging 1.00
Z1177:Clstn3 UTSW 6 124,426,740 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- ACACAAGCATGCGCCATTG -3'
(R):5'- CAAATTGCCCAGGTATGCTG -3'

Sequencing Primer
(F):5'- TGCGCCATTGCAGAGTC -3'
(R):5'- ATGCTGGGTTCTGCTGACCC -3'
Posted On 2020-01-23