Incidental Mutation 'R3934:Clstn3'
ID 306938
Institutional Source Beutler Lab
Gene Symbol Clstn3
Ensembl Gene ENSMUSG00000008153
Gene Name calsyntenin 3
Synonyms alcadein-beta, Cst-3, CSTN3
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3934 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 124430759-124464794 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) G to A at 124457942 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 338 (T338I)
Ref Sequence ENSEMBL: ENSMUSP00000108142 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000008297] [ENSMUST00000112523] [ENSMUST00000150774]
AlphaFold Q99JH7
Predicted Effect probably damaging
Transcript: ENSMUST00000008297
AA Change: T375I

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000008297
Gene: ENSMUSG00000008153
AA Change: T375I

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 damaging
Transcript: ENSMUST00000112523
AA Change: T338I

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000108142
Gene: ENSMUSG00000008153
AA Change: T338I

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
Predicted Effect probably benign
Transcript: ENSMUST00000150774
SMART Domains Protein: ENSMUSP00000145422
Gene: ENSMUSG00000008153

DomainStartEndE-ValueType
Blast:CA 13 64 4e-31 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156040
Meta Mutation Damage Score 0.3507 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.5%
Validation Efficiency 100% (40/40)
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: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5730507C01Rik T A 12: 18,534,081 Y381N possibly damaging Het
Adgrf3 T C 5: 30,200,434 probably benign Het
Adgrv1 A G 13: 81,475,047 F3819S probably benign Het
Aig1 T C 10: 13,801,912 D112G probably damaging Het
Akap6 C T 12: 53,140,444 T1547M possibly damaging Het
Alk T A 17: 72,205,954 I337F probably damaging Het
C2cd5 C T 6: 143,041,380 V499I possibly damaging Het
Capn11 A T 17: 45,634,287 probably benign Het
Cmbl A G 15: 31,589,787 D221G possibly damaging Het
Enpp2 A G 15: 54,845,921 V766A probably benign Het
Fastk G T 5: 24,442,259 S317* probably null Het
Fgfr1op2 T A 6: 146,595,171 probably benign Het
Gpr85 A G 6: 13,836,045 F287L probably benign Het
Hectd4 G A 5: 121,320,101 probably null Het
Hmcn2 T A 2: 31,380,484 probably null Het
Hspbp1 A T 7: 4,664,595 M271K probably benign Het
Itgb6 G A 2: 60,611,411 T685M possibly damaging Het
Itih5 G A 2: 10,245,544 V685I probably damaging Het
Kalrn T C 16: 34,310,531 S421G probably benign Het
Mcm2 G A 6: 88,893,008 R60C probably damaging Het
Mitf C T 6: 97,993,253 P54S probably damaging Het
Perm1 A G 4: 156,219,170 T724A probably benign Het
Pex5l T C 3: 33,007,172 E176G probably damaging Het
Polk A T 13: 96,501,635 M192K possibly damaging Het
Polr3a T C 14: 24,476,101 I401V probably benign Het
Prpf38b T C 3: 108,904,425 probably benign Het
Sema3c T C 5: 17,681,940 S330P probably damaging Het
Slc16a7 C A 10: 125,230,843 R309L probably damaging Het
Slc35f1 C T 10: 53,108,218 T358I probably damaging Het
Slc39a12 T A 2: 14,434,363 probably benign Het
Sod3 T C 5: 52,368,645 S229P probably benign Het
Sorcs3 T A 19: 48,713,504 V608D probably damaging Het
Spink5 G T 18: 44,016,427 K958N probably damaging Het
Ttc7 A C 17: 87,370,738 probably benign Het
Ush2a T A 1: 188,263,511 probably null Het
Vmn2r19 T A 6: 123,315,669 D223E probably damaging Het
Vwf T A 6: 125,555,499 S87T probably damaging Het
Wdr35 G T 12: 9,008,014 G513C probably damaging Het
Other mutations in Clstn3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01068:Clstn3 APN 6 124,462,139 (GRCm38) missense probably damaging 1.00
IGL01415:Clstn3 APN 6 124,438,822 (GRCm38) nonsense probably null
IGL01521:Clstn3 APN 6 124,458,031 (GRCm38) nonsense probably null
IGL01537:Clstn3 APN 6 124,431,600 (GRCm38) missense possibly damaging 0.91
IGL01729:Clstn3 APN 6 124,449,794 (GRCm38) missense probably benign 0.06
IGL01879:Clstn3 APN 6 124,438,810 (GRCm38) missense probably damaging 1.00
IGL01998:Clstn3 APN 6 124,458,663 (GRCm38) missense probably damaging 1.00
IGL03130:Clstn3 APN 6 124,459,263 (GRCm38) missense probably damaging 0.98
IGL03405:Clstn3 APN 6 124,438,368 (GRCm38) missense possibly damaging 0.95
PIT4403001:Clstn3 UTSW 6 124,458,023 (GRCm38) missense probably damaging 1.00
R0049:Clstn3 UTSW 6 124,459,853 (GRCm38) missense possibly damaging 0.87
R0049:Clstn3 UTSW 6 124,459,853 (GRCm38) missense possibly damaging 0.87
R0208:Clstn3 UTSW 6 124,432,169 (GRCm38) splice site probably benign
R0276:Clstn3 UTSW 6 124,431,740 (GRCm38) splice site probably benign
R0440:Clstn3 UTSW 6 124,451,413 (GRCm38) missense probably damaging 1.00
R0612:Clstn3 UTSW 6 124,449,500 (GRCm38) missense probably damaging 0.98
R1200:Clstn3 UTSW 6 124,459,170 (GRCm38) missense probably damaging 1.00
R1224:Clstn3 UTSW 6 124,457,919 (GRCm38) missense probably benign
R1378:Clstn3 UTSW 6 124,438,419 (GRCm38) missense probably damaging 1.00
R1491:Clstn3 UTSW 6 124,437,490 (GRCm38) missense possibly damaging 0.51
R1495:Clstn3 UTSW 6 124,449,917 (GRCm38) missense probably benign 0.00
R1511:Clstn3 UTSW 6 124,462,169 (GRCm38) missense probably damaging 1.00
R1655:Clstn3 UTSW 6 124,437,427 (GRCm38) missense probably damaging 1.00
R1731:Clstn3 UTSW 6 124,431,632 (GRCm38) missense probably benign 0.04
R1734:Clstn3 UTSW 6 124,436,814 (GRCm38) splice site probably benign
R1751:Clstn3 UTSW 6 124,431,999 (GRCm38) missense probably damaging 1.00
R1954:Clstn3 UTSW 6 124,459,298 (GRCm38) missense possibly damaging 0.94
R2133:Clstn3 UTSW 6 124,449,503 (GRCm38) missense probably benign
R2192:Clstn3 UTSW 6 124,459,207 (GRCm38) missense probably damaging 1.00
R2314:Clstn3 UTSW 6 124,450,717 (GRCm38) missense probably benign 0.39
R2874:Clstn3 UTSW 6 124,438,335 (GRCm38) missense probably damaging 1.00
R3500:Clstn3 UTSW 6 124,431,711 (GRCm38) missense probably benign 0.01
R3761:Clstn3 UTSW 6 124,457,876 (GRCm38) missense possibly damaging 0.54
R3878:Clstn3 UTSW 6 124,457,942 (GRCm38) missense probably damaging 0.97
R3927:Clstn3 UTSW 6 124,451,368 (GRCm38) missense probably damaging 1.00
R3935:Clstn3 UTSW 6 124,457,942 (GRCm38) missense probably damaging 0.97
R4063:Clstn3 UTSW 6 124,449,833 (GRCm38) missense possibly damaging 0.51
R4402:Clstn3 UTSW 6 124,456,980 (GRCm38) missense probably damaging 0.96
R4534:Clstn3 UTSW 6 124,459,220 (GRCm38) missense probably damaging 1.00
R4785:Clstn3 UTSW 6 124,437,372 (GRCm38) splice site probably null
R4834:Clstn3 UTSW 6 124,431,953 (GRCm38) splice site probably null
R5921:Clstn3 UTSW 6 124,431,580 (GRCm38) utr 3 prime probably benign
R5932:Clstn3 UTSW 6 124,438,332 (GRCm38) missense probably benign 0.01
R6025:Clstn3 UTSW 6 124,431,664 (GRCm38) missense possibly damaging 0.73
R6101:Clstn3 UTSW 6 124,461,670 (GRCm38) missense probably damaging 1.00
R6360:Clstn3 UTSW 6 124,438,429 (GRCm38) missense possibly damaging 0.88
R6578:Clstn3 UTSW 6 124,450,704 (GRCm38) critical splice donor site probably null
R6813:Clstn3 UTSW 6 124,436,935 (GRCm38) missense probably benign 0.00
R7380:Clstn3 UTSW 6 124,456,989 (GRCm38) missense probably benign 0.01
R7419:Clstn3 UTSW 6 124,458,129 (GRCm38) missense probably benign 0.05
R7625:Clstn3 UTSW 6 124,437,418 (GRCm38) nonsense probably null
R7780:Clstn3 UTSW 6 124,462,202 (GRCm38) missense probably damaging 0.98
R7936:Clstn3 UTSW 6 124,432,013 (GRCm38) missense possibly damaging 0.73
R7939:Clstn3 UTSW 6 124,462,199 (GRCm38) missense probably damaging 1.00
R8047:Clstn3 UTSW 6 124,432,013 (GRCm38) missense possibly damaging 0.73
R8079:Clstn3 UTSW 6 124,459,804 (GRCm38) missense probably damaging 1.00
R8085:Clstn3 UTSW 6 124,458,724 (GRCm38) missense probably benign 0.23
R8299:Clstn3 UTSW 6 124,437,373 (GRCm38) critical splice donor site probably null
R8406:Clstn3 UTSW 6 124,462,177 (GRCm38) missense probably damaging 1.00
R8685:Clstn3 UTSW 6 124,456,908 (GRCm38) missense probably damaging 1.00
R9045:Clstn3 UTSW 6 124,431,962 (GRCm38) missense probably damaging 0.98
R9209:Clstn3 UTSW 6 124,431,612 (GRCm38) missense probably benign 0.02
R9264:Clstn3 UTSW 6 124,459,768 (GRCm38) missense probably damaging 1.00
R9268:Clstn3 UTSW 6 124,456,921 (GRCm38) missense probably damaging 0.99
R9443:Clstn3 UTSW 6 124,451,399 (GRCm38) missense probably damaging 1.00
RF014:Clstn3 UTSW 6 124,459,266 (GRCm38) nonsense probably null
X0066:Clstn3 UTSW 6 124,449,811 (GRCm38) missense probably benign 0.13
Z1176:Clstn3 UTSW 6 124,459,200 (GRCm38) missense probably damaging 1.00
Z1177:Clstn3 UTSW 6 124,449,781 (GRCm38) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- CCTGCCAACAGTACTTATTGGG -3'
(R):5'- AGAGGAGATGAATTGTTTCCTTTCC -3'

Sequencing Primer
(F):5'- CCAACAGTACTTATTGGGTAACGGC -3'
(R):5'- CCTTTGGGGCATCTGCAG -3'
Posted On 2015-04-17