Incidental Mutation 'R7390:Shank3'
ID 573389
Institutional Source Beutler Lab
Gene Symbol Shank3
Ensembl Gene ENSMUSG00000022623
Gene Name SH3 and multiple ankyrin repeat domains 3
Synonyms ProSAP2
MMRRC Submission 045472-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.179) question?
Stock # R7390 (G1)
Quality Score 225.009
Status Validated
Chromosome 15
Chromosomal Location 89383826-89444464 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 89433515 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Arginine at position 1420 (L1420R)
Ref Sequence ENSEMBL: ENSMUSP00000104932 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000039074] [ENSMUST00000109309] [ENSMUST00000229559] [ENSMUST00000230807]
AlphaFold Q4ACU6
Predicted Effect
SMART Domains Protein: ENSMUSP00000048062
Gene: ENSMUSG00000022623
AA Change: L1345R

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 probably benign
Transcript: ENSMUST00000109309
AA Change: L1420R

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000104932
Gene: ENSMUSG00000022623
AA Change: L1420R

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 probably benign
Transcript: ENSMUST00000229559
Predicted Effect probably benign
Transcript: ENSMUST00000230807
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 97% (66/68)
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930486L24Rik A T 13: 60,992,152 (GRCm39) D291E probably benign Het
Abca9 C T 11: 110,036,487 (GRCm39) V541I probably benign Het
Adamts15 A T 9: 30,822,404 (GRCm39) probably null Het
Adgrg7 A G 16: 56,553,207 (GRCm39) I630T probably damaging Het
Ahnak A G 19: 8,980,569 (GRCm39) I618V probably benign Het
Amotl2 T A 9: 102,608,889 (GRCm39) V801E probably damaging Het
Ankrd17 T C 5: 90,430,779 (GRCm39) T1002A probably benign Het
Bmp7 C T 2: 172,711,998 (GRCm39) D409N probably damaging Het
Bpifb2 A G 2: 153,731,726 (GRCm39) N293S possibly damaging Het
Ccdc162 A G 10: 41,510,044 (GRCm39) C854R probably benign Het
Ccdc171 A G 4: 83,736,304 (GRCm39) E1225G probably damaging Het
Cep350 T C 1: 155,741,833 (GRCm39) E2146G possibly damaging Het
Ces1a A C 8: 93,771,469 (GRCm39) probably null Het
Cfap45 T G 1: 172,368,925 (GRCm39) D444E probably benign Het
Cfap61 T C 2: 145,843,802 (GRCm39) V296A probably benign Het
Cgnl1 C T 9: 71,552,931 (GRCm39) R1011H probably benign Het
Cops4 C T 5: 100,691,741 (GRCm39) R347C probably damaging Het
D16Ertd472e G T 16: 78,344,576 (GRCm39) D177E probably benign Het
Dcdc2a T C 13: 25,291,600 (GRCm39) V195A possibly damaging Het
Dipk2a A G 9: 94,419,436 (GRCm39) S165P probably damaging Het
Dpagt1 G A 9: 44,243,319 (GRCm39) V285I probably benign Het
Dspp G T 5: 104,323,552 (GRCm39) A232S probably damaging Het
Efcab3 T C 11: 104,615,411 (GRCm39) I726T possibly damaging Het
Ephx2 G A 14: 66,347,904 (GRCm39) Het
Fat1 T C 8: 45,405,511 (GRCm39) V754A possibly damaging Het
Fstl3 G A 10: 79,615,865 (GRCm39) C117Y probably damaging Het
Gldc A T 19: 30,077,314 (GRCm39) S953T possibly damaging Het
Gm1123 T C 9: 98,893,033 (GRCm39) N315S probably benign Het
Golga2 A G 2: 32,178,202 (GRCm39) E37G Het
Gpr139 T A 7: 118,743,835 (GRCm39) Q250L probably benign Het
Grik3 C T 4: 125,543,532 (GRCm39) R283C probably damaging Het
Haao A C 17: 84,154,081 (GRCm39) V22G probably damaging Het
Hspg2 T A 4: 137,266,490 (GRCm39) F1884I probably damaging Het
Hyal3 G A 9: 107,462,166 (GRCm39) G67S probably damaging Het
Kbtbd3 T A 9: 4,330,424 (GRCm39) I266K probably benign Het
Klhl26 A C 8: 70,905,499 (GRCm39) L137R probably damaging Het
Krt15 A T 11: 100,026,386 (GRCm39) V100E possibly damaging Het
Lars1 A G 18: 42,343,083 (GRCm39) probably null Het
Lats1 C T 10: 7,577,859 (GRCm39) Q328* probably null Het
Lingo3 G A 10: 80,670,463 (GRCm39) T489I probably damaging Het
Lmtk2 T C 5: 144,066,261 (GRCm39) V65A possibly damaging Het
Lysmd1 T C 3: 95,045,795 (GRCm39) S211P probably damaging Het
Med15 C T 16: 17,540,626 (GRCm39) S21N unknown Het
Nav1 T C 1: 135,512,656 (GRCm39) T135A probably benign Het
Nt5c1a G C 4: 123,102,272 (GRCm39) R66T probably benign Het
Pclo T C 5: 14,732,024 (GRCm39) Y3509H unknown Het
Pkp4 G A 2: 59,140,484 (GRCm39) G397R possibly damaging Het
Ppp1r21 G A 17: 88,856,958 (GRCm39) A138T probably benign Het
Pum3 A T 19: 27,401,642 (GRCm39) V136D probably benign Het
Rab11fip3 A T 17: 26,287,126 (GRCm39) D342E possibly damaging Het
Rcvrn T A 11: 67,590,883 (GRCm39) W156R probably damaging Het
Rspry1 C T 8: 95,349,813 (GRCm39) T67I probably benign Het
Serpina1d T C 12: 103,734,037 (GRCm39) D89G possibly damaging Het
Sgsm3 T A 15: 80,893,021 (GRCm39) V366E possibly damaging Het
Sirpb1b A T 3: 15,608,100 (GRCm39) L215* probably null Het
Slc16a13 C T 11: 70,109,797 (GRCm39) V235I probably benign Het
Slc16a14 T C 1: 84,907,187 (GRCm39) D29G probably benign Het
Speer1a T C 5: 11,394,879 (GRCm39) V122A probably benign Het
Spns2 T A 11: 72,347,704 (GRCm39) T329S possibly damaging Het
Sufu G A 19: 46,439,108 (GRCm39) probably null Het
Tll2 A G 19: 41,108,608 (GRCm39) probably null Het
Trim10 G A 17: 37,180,773 (GRCm39) M1I probably null Het
Trim42 A C 9: 97,241,182 (GRCm39) N683K probably damaging Het
Trmt5 A G 12: 73,328,394 (GRCm39) S270P probably damaging Het
Vmn1r59 C A 7: 5,456,986 (GRCm39) R258L possibly damaging Het
Vmn2r32 A G 7: 7,482,851 (GRCm39) L41S probably benign Het
Vmn2r93 A T 17: 18,525,329 (GRCm39) E329V probably damaging Het
Ywhae G T 11: 75,655,487 (GRCm39) E253* probably null 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
R5543:Shank3 UTSW 15 89,416,557 (GRCm39) missense probably damaging 1.00
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
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'- GAGCTGGTATTCGCTGTGAACC -3'
(R):5'- GTGGCTTCTCGAGTAGAAAAGTGTG -3'

Sequencing Primer
(F):5'- GTATTCGCTGTGAACCTGCCAC -3'
(R):5'- TCTCGAGTAGAAAAGTGTGTCCATCG -3'
Posted On 2019-09-13