Incidental Mutation 'R9209:Clstn3'
ID 698707
Institutional Source Beutler Lab
Gene Symbol Clstn3
Ensembl Gene ENSMUSG00000008153
Gene Name calsyntenin 3
Synonyms Cst-3, CSTN3, alcadein-beta
MMRRC Submission
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9209 (G1)
Quality Score 203.009
Status Validated
Chromosome 6
Chromosomal Location 124407715-124441743 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 124408571 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 951 (S951G)
Ref Sequence ENSEMBL: ENSMUSP00000008297 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000008297] [ENSMUST00000112523]
AlphaFold Q99JH7
Predicted Effect probably benign
Transcript: ENSMUST00000008297
AA Change: S951G

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000008297
Gene: ENSMUSG00000008153
AA Change: S951G

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 probably benign
Transcript: ENSMUST00000112523
AA Change: S914G

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000108142
Gene: ENSMUSG00000008153
AA Change: S914G

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 96% (73/76)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610021A01Rik T A 7: 41,275,837 (GRCm39) N513K possibly damaging Het
Actl6a T A 3: 32,779,469 (GRCm39) I399N probably damaging Het
Adamts5 A G 16: 85,666,971 (GRCm39) V507A probably damaging Het
Ap3d1 A G 10: 80,554,918 (GRCm39) V469A probably benign Het
Arhgef4 G T 1: 34,764,241 (GRCm39) probably null Het
Arhgef4 A T 1: 34,849,576 (GRCm39) Q389L probably benign Het
Atad2 A G 15: 57,980,194 (GRCm39) V106A possibly damaging Het
Azin2 T C 4: 128,841,341 (GRCm39) E275G probably damaging Het
Bhlhe23 A G 2: 180,418,143 (GRCm39) S132P probably damaging Het
Capn12 A G 7: 28,581,243 (GRCm39) Y32C probably damaging Het
Celsr2 A T 3: 108,321,349 (GRCm39) S488T probably benign Het
Cenpx A G 11: 120,602,582 (GRCm39) V27A possibly damaging Het
Clca3a2 G A 3: 144,778,005 (GRCm39) P760L probably benign Het
Clybl C A 14: 122,621,670 (GRCm39) P286Q probably benign Het
Cmya5 T A 13: 93,226,866 (GRCm39) M2741L probably benign Het
Cntnap2 G A 6: 47,026,183 (GRCm39) G944E probably damaging Het
Col8a1 A C 16: 57,447,283 (GRCm39) Y742* probably null Het
Crb1 T C 1: 139,171,051 (GRCm39) K780E probably damaging Het
Crygc T A 1: 65,112,376 (GRCm39) Y66F probably benign Het
Cyp2b9 G A 7: 25,873,004 (GRCm39) G49E possibly damaging Het
D130043K22Rik T C 13: 25,041,090 (GRCm39) S171P possibly damaging Het
Dhx36 T C 3: 62,378,895 (GRCm39) I890V probably benign Het
Dpp9 C T 17: 56,512,765 (GRCm39) G148S probably damaging Het
Eml6 G T 11: 29,781,175 (GRCm39) S619Y probably damaging Het
Enpp4 A T 17: 44,412,252 (GRCm39) L319* probably null Het
Esyt1 T C 10: 128,361,356 (GRCm39) S113G probably benign Het
Fat1 A G 8: 45,404,791 (GRCm39) D514G possibly damaging Het
Fbxo16 G A 14: 65,524,594 (GRCm39) R38Q probably damaging Het
Fchsd1 A T 18: 38,092,706 (GRCm39) M668K unknown Het
Gpr149 C T 3: 62,511,093 (GRCm39) S302N probably benign Het
Gsap A G 5: 21,433,064 (GRCm39) K258E probably benign Het
Helq C A 5: 100,939,218 (GRCm39) V443F probably benign Het
Helq T A 5: 100,939,219 (GRCm39) K442N probably damaging Het
Ighv1-37 T C 12: 114,860,123 (GRCm39) E29G possibly damaging Het
Ighv1-9 C A 12: 114,547,620 (GRCm39) M1I probably null Het
Itga6 T G 2: 71,671,477 (GRCm39) F743V probably benign Het
Lpin1 C A 12: 16,588,548 (GRCm39) D881Y Het
Lypd8 T A 11: 58,273,640 (GRCm39) C40S possibly damaging Het
Macf1 C T 4: 123,326,227 (GRCm39) R5092Q probably damaging Het
Mcm7 A G 5: 138,166,593 (GRCm39) probably null Het
Micall2 G A 5: 139,696,170 (GRCm39) T831I unknown Het
Myo18b A T 5: 113,022,927 (GRCm39) M155K unknown Het
Nckap5 T A 1: 125,867,928 (GRCm39) H201L unknown Het
Ndst2 A T 14: 20,779,240 (GRCm39) D333E possibly damaging Het
Nlgn1 A G 3: 25,966,804 (GRCm39) probably null Het
Nup188 T G 2: 30,232,397 (GRCm39) Y1483D probably benign Het
Or4c109 A C 2: 88,818,057 (GRCm39) L163* probably null Het
Or52ae9 T A 7: 103,390,319 (GRCm39) S43C probably benign Het
Or52n4b A C 7: 108,144,664 (GRCm39) I311L probably benign Het
Or5p66 T A 7: 107,885,526 (GRCm39) Y269F probably benign Het
Or8g33 T A 9: 39,337,635 (GRCm39) H244L probably damaging Het
Peg3 A C 7: 6,711,226 (GRCm39) I1332S possibly damaging Het
Piezo2 T C 18: 63,154,372 (GRCm39) K2469R probably damaging Het
Pik3cg T C 12: 32,247,312 (GRCm39) M804V probably damaging Het
Polq A T 16: 36,869,011 (GRCm39) I794F possibly damaging Het
Rasgef1b A G 5: 99,370,191 (GRCm39) V437A probably benign Het
Rdm1 T A 11: 101,518,857 (GRCm39) D21E probably benign Het
Ripk4 G T 16: 97,551,311 (GRCm39) Q219K possibly damaging Het
Ropn1l T C 15: 31,441,471 (GRCm39) I217V Het
Sdf2 T C 11: 78,136,858 (GRCm39) S13P unknown Het
Selenbp1 A G 3: 94,847,079 (GRCm39) T202A probably benign Het
Slfn5 T C 11: 82,850,933 (GRCm39) F410S possibly damaging Het
Srrm2 A G 17: 24,039,880 (GRCm39) T2175A probably benign Het
St6galnac3 T C 3: 153,117,360 (GRCm39) Y121C possibly damaging Het
Stat1 A G 1: 52,184,337 (GRCm39) N417S probably benign Het
Tead1 T C 7: 112,475,378 (GRCm39) F276L probably damaging Het
Teddm3 A T 16: 20,971,737 (GRCm39) S277R probably benign Het
Tmc2 A G 2: 130,103,317 (GRCm39) probably null Het
Tmem156 G A 5: 65,231,127 (GRCm39) L248F probably damaging Het
Tnn T C 1: 159,953,986 (GRCm39) S590G probably benign Het
Trmt44 A G 5: 35,731,422 (GRCm39) probably null Het
Upp2 T A 2: 58,668,022 (GRCm39) Y238* probably null Het
Usp32 T C 11: 84,930,838 (GRCm39) T531A probably damaging Het
Vmn2r78 A T 7: 86,569,431 (GRCm39) D108V probably benign Het
Wdfy3 G T 5: 102,078,830 (GRCm39) A824E probably benign Het
Xylt1 T C 7: 117,255,870 (GRCm39) V814A probably benign Het
Zfy1 C T Y: 732,990 (GRCm39) R281H unknown 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
R8047:Clstn3 UTSW 6 124,408,972 (GRCm39) missense possibly damaging 0.73
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
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'- AGTATGCTGCCACAGGTAGG -3'
(R):5'- CAATGGCGCATGCTTGTGTG -3'

Sequencing Primer
(F):5'- TGCCACAGGTAGGCTACAG -3'
(R):5'- CTCAAGGAGAGGTTCTGCC -3'
Posted On 2022-02-07