Incidental Mutation 'R5543:Shank3'
ID 436123
Institutional Source Beutler Lab
Gene Symbol Shank3
Ensembl Gene ENSMUSG00000022623
Gene Name SH3 and multiple ankyrin repeat domains 3
Synonyms ProSAP2
MMRRC Submission 043101-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.176) question?
Stock # R5543 (G1)
Quality Score 225
Status Not validated
Chromosome 15
Chromosomal Location 89383826-89444464 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 89416557 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 232 (V232A)
Ref Sequence ENSEMBL: ENSMUSP00000155608 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000039074] [ENSMUST00000066545] [ENSMUST00000109309] [ENSMUST00000167173] [ENSMUST00000229559] [ENSMUST00000230807]
AlphaFold Q4ACU6
Predicted Effect possibly damaging
Transcript: ENSMUST00000039074
AA Change: V640A

PolyPhen 2 Score 0.566 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000048062
Gene: ENSMUSG00000022623
AA Change: V640A

DomainStartEndE-ValueType
ANK 182 211 1.54e-1 SMART
ANK 215 245 3.36e2 SMART
ANK 249 278 2.47e0 SMART
ANK 282 311 3.71e-4 SMART
ANK 315 345 5.03e2 SMART
low complexity region 434 462 N/A INTRINSIC
SH3 473 528 1.28e-14 SMART
PDZ 579 664 3.95e-13 SMART
low complexity region 672 684 N/A INTRINSIC
low complexity region 813 843 N/A INTRINSIC
low complexity region 857 869 N/A INTRINSIC
low complexity region 905 923 N/A INTRINSIC
low complexity region 1078 1092 N/A INTRINSIC
low complexity region 1109 1121 N/A INTRINSIC
low complexity region 1173 1194 N/A INTRINSIC
low complexity region 1235 1252 N/A INTRINSIC
low complexity region 1266 1278 N/A INTRINSIC
low complexity region 1318 1332 N/A INTRINSIC
low complexity region 1341 1355 N/A INTRINSIC
low complexity region 1370 1395 N/A INTRINSIC
low complexity region 1409 1427 N/A INTRINSIC
low complexity region 1552 1558 N/A INTRINSIC
low complexity region 1584 1599 N/A INTRINSIC
low complexity region 1626 1658 N/A INTRINSIC
SAM 1664 1730 3.08e-18 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000066545
SMART Domains Protein: ENSMUSP00000064477
Gene: ENSMUSG00000022623

DomainStartEndE-ValueType
ANK 109 138 1.54e-1 SMART
ANK 142 172 3.36e2 SMART
ANK 176 205 2.47e0 SMART
ANK 209 238 3.71e-4 SMART
ANK 242 272 5.03e2 SMART
low complexity region 361 389 N/A INTRINSIC
SH3 400 455 1.28e-14 SMART
PDZ 506 591 3.95e-13 SMART
low complexity region 599 611 N/A INTRINSIC
low complexity region 625 636 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000109309
AA Change: V715A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000104932
Gene: ENSMUSG00000022623
AA Change: V715A

DomainStartEndE-ValueType
low complexity region 5 55 N/A INTRINSIC
Pfam:FERM_f0 84 167 2.5e-14 PFAM
ANK 257 286 1.54e-1 SMART
ANK 290 320 3.36e2 SMART
ANK 324 353 2.47e0 SMART
ANK 357 386 3.71e-4 SMART
ANK 390 420 5.03e2 SMART
low complexity region 509 537 N/A INTRINSIC
SH3 548 603 1.28e-14 SMART
PDZ 654 739 3.95e-13 SMART
low complexity region 747 759 N/A INTRINSIC
low complexity region 888 918 N/A INTRINSIC
low complexity region 932 944 N/A INTRINSIC
low complexity region 980 998 N/A INTRINSIC
low complexity region 1153 1167 N/A INTRINSIC
low complexity region 1184 1196 N/A INTRINSIC
low complexity region 1248 1269 N/A INTRINSIC
low complexity region 1310 1327 N/A INTRINSIC
low complexity region 1341 1353 N/A INTRINSIC
low complexity region 1393 1407 N/A INTRINSIC
low complexity region 1416 1430 N/A INTRINSIC
low complexity region 1445 1470 N/A INTRINSIC
low complexity region 1484 1502 N/A INTRINSIC
low complexity region 1627 1633 N/A INTRINSIC
low complexity region 1659 1674 N/A INTRINSIC
low complexity region 1701 1733 N/A INTRINSIC
SAM 1739 1805 3.08e-18 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123799
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154240
Predicted Effect probably benign
Transcript: ENSMUST00000167173
SMART Domains Protein: ENSMUSP00000132229
Gene: ENSMUSG00000022623

DomainStartEndE-ValueType
low complexity region 57 66 N/A INTRINSIC
low complexity region 80 91 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000229559
AA Change: V232A

PolyPhen 2 Score 0.954 (Sensitivity: 0.79; Specificity: 0.95)
Predicted Effect probably damaging
Transcript: ENSMUST00000230807
AA Change: V232A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.7%
Validation Efficiency
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 Shank gene family. Shank proteins are multidomain scaffold proteins of the postsynaptic density that connect neurotransmitter receptors, ion channels, and other membrane proteins to the actin cytoskeleton and G-protein-coupled signaling pathways. Shank proteins also play a role in synapse formation and dendritic spine maturation. Mutations in this gene are a cause of autism spectrum disorder (ASD), which is characterized by impairments in social interaction and communication, and restricted behavioral patterns and interests. Mutations in this gene also cause schizophrenia type 15, and are a major causative factor in the neurological symptoms of 22q13.3 deletion syndrome, which is also known as Phelan-McDermid syndrome. Additional isoforms have been described for this gene but they have not yet been experimentally verified. [provided by RefSeq, Mar 2012]
PHENOTYPE: Mice carrying various deletions of exons encoding the ankyrin repeats (exons 4-9) exhibit a range of synaptic and autism-related impairments. Homozygotes lacking exon 9 show altered excitation/inhibition balance, increased rearing, and mildly impaired spatial memory. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9130023H24Rik C A 7: 127,836,353 (GRCm39) S80I probably benign Het
Aak1 T C 6: 86,959,627 (GRCm39) probably null Het
Abcc6 A G 7: 45,638,960 (GRCm39) probably null Het
Acvr1 A G 2: 58,353,157 (GRCm39) S268P probably damaging Het
Apod T C 16: 31,122,351 (GRCm39) probably null Het
Atp5po T C 16: 91,723,418 (GRCm39) I58V probably benign Het
AU040320 C T 4: 126,735,017 (GRCm39) T777M probably damaging Het
Ccne2 A T 4: 11,194,026 (GRCm39) N89I probably benign Het
Cspg4b C A 13: 113,457,407 (GRCm39) T1151K probably damaging Het
Dnah7a A G 1: 53,543,228 (GRCm39) V2314A probably damaging Het
Dop1b T C 16: 93,595,808 (GRCm39) S1881P probably damaging Het
E4f1 A G 17: 24,666,336 (GRCm39) V24A possibly damaging Het
Esrrg A T 1: 187,882,451 (GRCm39) D236V probably damaging Het
Fam240b T A 13: 64,633,736 (GRCm39) I27F possibly damaging Het
Fat1 T A 8: 45,476,516 (GRCm39) I1854N probably damaging Het
Fchsd2 T C 7: 100,920,906 (GRCm39) Y480H probably damaging Het
Fras1 A G 5: 96,676,394 (GRCm39) N47S probably benign Het
Gabrr3 T C 16: 59,253,870 (GRCm39) S196P probably damaging Het
Gbp8 T A 5: 105,165,696 (GRCm39) D319V possibly damaging Het
Hrh3 G T 2: 179,745,763 (GRCm39) A61E probably damaging Het
Idua T C 5: 108,818,095 (GRCm39) I89T probably benign Het
Ifitm3 T A 7: 140,589,730 (GRCm39) I108F unknown Het
Izumo4 T C 10: 80,538,668 (GRCm39) F40S probably damaging Het
Kifc2 A G 15: 76,551,242 (GRCm39) R679G probably damaging Het
Klk14 G A 7: 43,341,501 (GRCm39) C51Y probably damaging Het
Ldha A T 7: 46,500,314 (GRCm39) I171F possibly damaging Het
Lrfn4 T C 19: 4,662,191 (GRCm39) S609G probably benign Het
Mmp15 T C 8: 96,094,729 (GRCm39) F201S possibly damaging Het
Myof C T 19: 37,969,778 (GRCm39) V295I probably benign Het
Or1n2 C T 2: 36,797,369 (GRCm39) T137I possibly damaging Het
Or2z2 T A 11: 58,345,993 (GRCm39) M261L probably damaging Het
Or5m12 G T 2: 85,734,672 (GRCm39) A242D probably damaging Het
Parp14 T C 16: 35,655,137 (GRCm39) D1778G probably benign Het
Pcnt A T 10: 76,247,886 (GRCm39) D969E probably benign Het
Pibf1 A T 14: 99,350,428 (GRCm39) N192I probably benign Het
Pitpnm3 A G 11: 71,947,023 (GRCm39) F792S probably damaging Het
Pkd2 T A 5: 104,637,199 (GRCm39) I604N probably damaging Het
Pla2g15 T C 8: 106,887,775 (GRCm39) Y188H probably damaging Het
Plxnc1 G T 10: 94,700,636 (GRCm39) D643E probably benign Het
Prrc2c G A 1: 162,501,080 (GRCm39) P1241L probably damaging Het
Ptprd T C 4: 75,977,990 (GRCm39) E173G probably damaging Het
Shbg A G 11: 69,507,564 (GRCm39) I171T probably damaging Het
Slc22a14 A T 9: 119,002,674 (GRCm39) F404L probably benign Het
Slc37a3 C A 6: 39,331,960 (GRCm39) G158C probably damaging Het
Slfn9 C A 11: 82,873,207 (GRCm39) L565F probably damaging Het
Spmip10 G A 18: 56,727,760 (GRCm39) probably benign Het
Trank1 T A 9: 111,195,180 (GRCm39) M1068K probably damaging Het
Trbv15 A T 6: 41,118,187 (GRCm39) I15L probably benign Het
Ttn C T 2: 76,569,918 (GRCm39) V26992M probably damaging Het
Ttn A T 2: 76,641,587 (GRCm39) L5176Q possibly damaging Het
Ugt2b34 T A 5: 87,054,560 (GRCm39) I74F probably damaging Het
Vamp3 A G 4: 151,135,477 (GRCm39) L47P probably damaging Het
Zfp143 T A 7: 109,682,522 (GRCm39) C363* probably null Het
Zfp438 T C 18: 5,213,761 (GRCm39) E399G probably damaging Het
Other mutations in Shank3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01070:Shank3 APN 15 89,433,619 (GRCm39) missense probably damaging 1.00
IGL01469:Shank3 APN 15 89,405,477 (GRCm39) missense probably damaging 1.00
IGL01886:Shank3 APN 15 89,415,866 (GRCm39) missense probably damaging 1.00
IGL01934:Shank3 APN 15 89,434,049 (GRCm39) missense probably damaging 1.00
IGL01989:Shank3 APN 15 89,387,502 (GRCm39) splice site probably benign
IGL02004:Shank3 APN 15 89,387,502 (GRCm39) splice site probably benign
IGL02085:Shank3 APN 15 89,388,118 (GRCm39) critical splice donor site probably null
IGL02195:Shank3 APN 15 89,432,321 (GRCm39) missense probably damaging 1.00
IGL02354:Shank3 APN 15 89,388,536 (GRCm39) missense probably damaging 1.00
IGL02361:Shank3 APN 15 89,388,536 (GRCm39) missense probably damaging 1.00
IGL02541:Shank3 APN 15 89,385,613 (GRCm39) missense probably damaging 1.00
G1citation:Shank3 UTSW 15 89,415,830 (GRCm39) missense probably damaging 1.00
R0294:Shank3 UTSW 15 89,416,301 (GRCm39) missense probably damaging 1.00
R0468:Shank3 UTSW 15 89,433,478 (GRCm39) missense probably benign 0.28
R0483:Shank3 UTSW 15 89,427,442 (GRCm39) splice site probably benign
R0605:Shank3 UTSW 15 89,408,350 (GRCm39) missense possibly damaging 0.49
R0675:Shank3 UTSW 15 89,415,591 (GRCm39) missense possibly damaging 0.92
R1082:Shank3 UTSW 15 89,433,574 (GRCm39) missense probably damaging 1.00
R1576:Shank3 UTSW 15 89,387,866 (GRCm39) missense probably benign 0.11
R1702:Shank3 UTSW 15 89,384,099 (GRCm39) missense probably damaging 0.99
R1726:Shank3 UTSW 15 89,442,189 (GRCm39) missense probably damaging 1.00
R1958:Shank3 UTSW 15 89,387,351 (GRCm39) missense probably damaging 0.99
R1961:Shank3 UTSW 15 89,442,167 (GRCm39) missense possibly damaging 0.60
R2420:Shank3 UTSW 15 89,405,413 (GRCm39) nonsense probably null
R2513:Shank3 UTSW 15 89,432,889 (GRCm39) missense probably benign 0.05
R3917:Shank3 UTSW 15 89,387,587 (GRCm39) missense possibly damaging 0.77
R4163:Shank3 UTSW 15 89,433,797 (GRCm39) missense probably damaging 1.00
R4205:Shank3 UTSW 15 89,387,521 (GRCm39) missense probably damaging 1.00
R4434:Shank3 UTSW 15 89,387,562 (GRCm39) missense probably damaging 1.00
R4791:Shank3 UTSW 15 89,384,557 (GRCm39) missense probably damaging 1.00
R4816:Shank3 UTSW 15 89,427,318 (GRCm39) missense probably damaging 1.00
R4828:Shank3 UTSW 15 89,384,402 (GRCm39) intron probably benign
R4911:Shank3 UTSW 15 89,388,547 (GRCm39) missense probably damaging 1.00
R4997:Shank3 UTSW 15 89,433,901 (GRCm39) missense probably damaging 1.00
R5213:Shank3 UTSW 15 89,417,481 (GRCm39) missense possibly damaging 0.82
R5338:Shank3 UTSW 15 89,415,914 (GRCm39) splice site probably null
R5494:Shank3 UTSW 15 89,432,441 (GRCm39) missense probably damaging 0.99
R5654:Shank3 UTSW 15 89,405,529 (GRCm39) missense probably benign 0.07
R5900:Shank3 UTSW 15 89,387,593 (GRCm39) missense probably damaging 1.00
R5906:Shank3 UTSW 15 89,433,119 (GRCm39) missense probably damaging 1.00
R6385:Shank3 UTSW 15 89,405,578 (GRCm39) critical splice donor site probably null
R6432:Shank3 UTSW 15 89,387,616 (GRCm39) missense possibly damaging 0.75
R6724:Shank3 UTSW 15 89,416,656 (GRCm39) missense probably damaging 1.00
R6822:Shank3 UTSW 15 89,415,830 (GRCm39) missense probably damaging 1.00
R6845:Shank3 UTSW 15 89,432,528 (GRCm39) missense probably benign 0.00
R7088:Shank3 UTSW 15 89,387,728 (GRCm39) splice site probably null
R7390:Shank3 UTSW 15 89,433,515 (GRCm39) missense probably benign 0.05
R7808:Shank3 UTSW 15 89,433,083 (GRCm39) missense probably damaging 1.00
R7862:Shank3 UTSW 15 89,389,648 (GRCm39) missense possibly damaging 0.73
R8039:Shank3 UTSW 15 89,389,642 (GRCm39) missense probably damaging 1.00
R8090:Shank3 UTSW 15 89,389,661 (GRCm39) critical splice donor site probably null
R8170:Shank3 UTSW 15 89,433,043 (GRCm39) missense possibly damaging 0.69
R8189:Shank3 UTSW 15 89,433,439 (GRCm39) missense probably benign
R8246:Shank3 UTSW 15 89,417,549 (GRCm39) missense possibly damaging 0.90
R8515:Shank3 UTSW 15 89,387,775 (GRCm39) nonsense probably null
R8525:Shank3 UTSW 15 89,431,973 (GRCm39) missense probably damaging 0.99
R8537:Shank3 UTSW 15 89,416,418 (GRCm39) missense probably damaging 1.00
R8673:Shank3 UTSW 15 89,433,979 (GRCm39) missense probably damaging 1.00
R8826:Shank3 UTSW 15 89,433,598 (GRCm39) missense probably damaging 1.00
R8932:Shank3 UTSW 15 89,432,986 (GRCm39) missense possibly damaging 0.86
R8954:Shank3 UTSW 15 89,433,431 (GRCm39) missense possibly damaging 0.88
R8976:Shank3 UTSW 15 89,442,381 (GRCm39) missense probably damaging 1.00
R8992:Shank3 UTSW 15 89,432,888 (GRCm39) missense possibly damaging 0.95
R8994:Shank3 UTSW 15 89,417,416 (GRCm39) missense probably benign 0.27
R9130:Shank3 UTSW 15 89,442,419 (GRCm39) missense probably benign 0.19
R9258:Shank3 UTSW 15 89,388,521 (GRCm39) missense probably damaging 1.00
R9645:Shank3 UTSW 15 89,409,453 (GRCm39) missense possibly damaging 0.96
RF020:Shank3 UTSW 15 89,384,593 (GRCm39) missense probably benign 0.20
Z1177:Shank3 UTSW 15 89,442,525 (GRCm39) makesense probably null
Predicted Primers PCR Primer
(F):5'- CCCTGCACTCCAATACCTTGAG -3'
(R):5'- AGCAATGTGATGTCAGCTGTG -3'

Sequencing Primer
(F):5'- GCACTCCAATACCTTGAGTCTGTAG -3'
(R):5'- TGTCAGCTGTGTAGGATCAGAAATG -3'
Posted On 2016-10-24