Incidental Mutation 'R4939:Sncaip'
ID 382964
Institutional Source Beutler Lab
Gene Symbol Sncaip
Ensembl Gene ENSMUSG00000024534
Gene Name synuclein, alpha interacting protein (synphilin)
Synonyms synphilin-1, SYPH1, 4933427B05Rik
MMRRC Submission 042538-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.193) question?
Stock # R4939 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 52900872-53049007 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 53040335 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Leucine at position 843 (Q843L)
Ref Sequence ENSEMBL: ENSMUSP00000137367 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025413] [ENSMUST00000115410] [ENSMUST00000163742] [ENSMUST00000177861] [ENSMUST00000178011] [ENSMUST00000178678] [ENSMUST00000179689] [ENSMUST00000179625] [ENSMUST00000178883] [ENSMUST00000180259]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000025413
AA Change: Q843L

PolyPhen 2 Score 0.532 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000025413
Gene: ENSMUSG00000024534
AA Change: Q843L

DomainStartEndE-ValueType
ANK 348 378 2.07e-2 SMART
ANK 383 412 1.04e2 SMART
ANK 418 447 5.03e2 SMART
ANK 455 484 4.26e-4 SMART
PDB:2KES|A 511 549 1e-9 PDB
low complexity region 550 571 N/A INTRINSIC
low complexity region 656 669 N/A INTRINSIC
low complexity region 673 686 N/A INTRINSIC
low complexity region 745 755 N/A INTRINSIC
low complexity region 792 803 N/A INTRINSIC
low complexity region 869 875 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000115410
AA Change: Q843L

PolyPhen 2 Score 0.390 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000111069
Gene: ENSMUSG00000024534
AA Change: Q843L

DomainStartEndE-ValueType
ANK 348 378 2.07e-2 SMART
ANK 383 412 1.04e2 SMART
ANK 418 447 5.03e2 SMART
ANK 455 484 4.26e-4 SMART
PDB:2KES|A 511 549 1e-9 PDB
low complexity region 550 571 N/A INTRINSIC
low complexity region 656 669 N/A INTRINSIC
low complexity region 673 686 N/A INTRINSIC
low complexity region 745 755 N/A INTRINSIC
low complexity region 792 803 N/A INTRINSIC
low complexity region 869 875 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000163742
AA Change: Q843L

PolyPhen 2 Score 0.390 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000127189
Gene: ENSMUSG00000024534
AA Change: Q843L

DomainStartEndE-ValueType
ANK 348 378 2.07e-2 SMART
ANK 383 412 1.04e2 SMART
ANK 418 447 5.03e2 SMART
ANK 455 484 4.26e-4 SMART
PDB:2KES|A 511 549 1e-9 PDB
low complexity region 550 571 N/A INTRINSIC
low complexity region 656 669 N/A INTRINSIC
low complexity region 673 686 N/A INTRINSIC
low complexity region 745 755 N/A INTRINSIC
low complexity region 792 803 N/A INTRINSIC
low complexity region 869 875 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000177861
Predicted Effect probably benign
Transcript: ENSMUST00000178011
AA Change: Q843L

PolyPhen 2 Score 0.390 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000137549
Gene: ENSMUSG00000024534
AA Change: Q843L

DomainStartEndE-ValueType
ANK 348 378 2.07e-2 SMART
ANK 383 412 1.04e2 SMART
ANK 418 447 5.03e2 SMART
ANK 455 484 4.26e-4 SMART
PDB:2KES|A 511 549 1e-9 PDB
low complexity region 550 571 N/A INTRINSIC
low complexity region 656 669 N/A INTRINSIC
low complexity region 673 686 N/A INTRINSIC
low complexity region 745 755 N/A INTRINSIC
low complexity region 792 803 N/A INTRINSIC
low complexity region 869 875 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000178678
AA Change: Q843L

PolyPhen 2 Score 0.532 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000137367
Gene: ENSMUSG00000024534
AA Change: Q843L

DomainStartEndE-ValueType
ANK 348 378 2.07e-2 SMART
ANK 383 412 1.04e2 SMART
ANK 418 447 5.03e2 SMART
ANK 455 484 4.26e-4 SMART
Pfam:SNCAIP_SNCA_bd 511 556 7.9e-30 PFAM
low complexity region 656 669 N/A INTRINSIC
low complexity region 673 686 N/A INTRINSIC
low complexity region 745 755 N/A INTRINSIC
low complexity region 792 803 N/A INTRINSIC
low complexity region 869 875 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000179689
AA Change: Q431L

PolyPhen 2 Score 0.201 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000137107
Gene: ENSMUSG00000024534
AA Change: Q431L

DomainStartEndE-ValueType
ANK 43 72 4.26e-4 SMART
PDB:2KES|A 99 137 6e-10 PDB
low complexity region 138 159 N/A INTRINSIC
low complexity region 244 257 N/A INTRINSIC
low complexity region 261 274 N/A INTRINSIC
low complexity region 333 343 N/A INTRINSIC
low complexity region 380 391 N/A INTRINSIC
low complexity region 457 463 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000179625
AA Change: Q783L

PolyPhen 2 Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000136838
Gene: ENSMUSG00000024534
AA Change: Q783L

DomainStartEndE-ValueType
ANK 358 387 5.03e2 SMART
ANK 395 424 4.26e-4 SMART
PDB:2KES|A 451 489 9e-10 PDB
low complexity region 490 511 N/A INTRINSIC
low complexity region 596 609 N/A INTRINSIC
low complexity region 613 626 N/A INTRINSIC
low complexity region 685 695 N/A INTRINSIC
low complexity region 732 743 N/A INTRINSIC
low complexity region 809 815 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000178883
Predicted Effect probably benign
Transcript: ENSMUST00000180259
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.4%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing several protein-protein interaction domains, including ankyrin-like repeats, a coiled-coil domain, and an ATP/GTP-binding motif. The encoded protein interacts with alpha-synuclein in neuronal tissue and may play a role in the formation of cytoplasmic inclusions and neurodegeneration. A mutation in this gene has been associated with Parkinson's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
Allele List at MGI
Other mutations in this stock
Total: 85 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamtsl1 A T 4: 86,161,962 (GRCm39) Y365F possibly damaging Het
Atp2a1 T C 7: 126,049,288 (GRCm39) M585V probably benign Het
Brca1 A G 11: 101,398,876 (GRCm39) V1572A probably benign Het
C1ql4 A T 15: 98,985,521 (GRCm39) M30K probably damaging Het
Ccdc73 A G 2: 104,822,502 (GRCm39) probably null Het
Cdk6 A T 5: 3,394,377 (GRCm39) D4V probably null Het
Celf3 ACAGCAGCAGCAGCAGCAGCAGCA ACAGCAGCAGCAGCAGCAGCA 3: 94,395,537 (GRCm39) probably benign Het
Clic4 T C 4: 134,950,852 (GRCm39) E113G probably benign Het
Creld1 C A 6: 113,465,140 (GRCm39) H122Q probably benign Het
Cyp4a29 G A 4: 115,104,873 (GRCm39) probably null Het
Dnaaf3 A T 7: 4,530,144 (GRCm39) S246R probably damaging Het
Dnah12 A T 14: 26,613,481 (GRCm39) T3925S probably damaging Het
Dnajc21 T A 15: 10,449,683 (GRCm39) D446V probably damaging Het
Dock8 A T 19: 25,099,764 (GRCm39) Y629F probably damaging Het
Duxf4 T C 10: 58,071,425 (GRCm39) N263S probably benign Het
E2f8 A T 7: 48,521,886 (GRCm39) N405K probably benign Het
Flg A G 3: 93,187,154 (GRCm39) N202S probably benign Het
Glyatl3 A G 17: 41,220,914 (GRCm39) probably null Het
Gm38999 A G 7: 43,077,885 (GRCm39) T63A possibly damaging Het
Grap A G 11: 61,551,124 (GRCm39) Y52C probably damaging Het
Haus2 T A 2: 120,449,517 (GRCm39) I187K probably damaging Het
Heatr5b T C 17: 79,069,689 (GRCm39) E1686G probably benign Het
Herc2 A G 7: 55,856,484 (GRCm39) D3944G probably damaging Het
Hexd A T 11: 121,098,542 (GRCm39) M9L probably benign Het
Hoxa3 T C 6: 52,147,656 (GRCm39) probably benign Het
Hspg2 A T 4: 137,235,342 (GRCm39) I126F probably damaging Het
Itpr1 T A 6: 108,417,519 (GRCm39) C123* probably null Het
Jmjd1c T A 10: 67,081,916 (GRCm39) N2346K possibly damaging Het
Kctd9 A G 14: 67,967,135 (GRCm39) Y37C probably damaging Het
Kmt5b A C 19: 3,865,245 (GRCm39) S747R possibly damaging Het
Krt26 T C 11: 99,225,522 (GRCm39) M320V probably benign Het
Lama1 T G 17: 68,044,470 (GRCm39) V123G possibly damaging Het
Lamc2 T C 1: 153,002,582 (GRCm39) D1103G probably damaging Het
Lepr A T 4: 101,590,635 (GRCm39) K71I possibly damaging Het
Llgl1 A T 11: 60,600,805 (GRCm39) probably null Het
Mcoln2 A T 3: 145,897,996 (GRCm39) H39L probably benign Het
Mtrex T C 13: 113,046,426 (GRCm39) D308G possibly damaging Het
Myh11 T A 16: 14,057,371 (GRCm39) T315S probably benign Het
Ncapd3 T C 9: 26,975,165 (GRCm39) probably null Het
Nlrp9b G T 7: 19,758,421 (GRCm39) V553F probably damaging Het
Nubpl A G 12: 52,227,878 (GRCm39) N129S probably damaging Het
Nup214 C A 2: 31,873,171 (GRCm39) T255K probably benign Het
Or10j3 T C 1: 173,031,030 (GRCm39) Y36H possibly damaging Het
Or2t46 G T 11: 58,472,037 (GRCm39) M122I probably damaging Het
Or2y17 A G 11: 49,231,376 (GRCm39) T6A probably benign Het
Or4d1 G T 11: 87,804,950 (GRCm39) P261T probably damaging Het
Or52z14 T C 7: 103,253,458 (GRCm39) V199A probably benign Het
Or5b3 T A 19: 13,388,219 (GRCm39) N95K probably benign Het
Orc3 G A 4: 34,593,126 (GRCm39) Q256* probably null Het
Pbrm1 A G 14: 30,783,580 (GRCm39) M566V probably damaging Het
Pde6b A G 5: 108,569,363 (GRCm39) I357V probably benign Het
Pkdrej A G 15: 85,704,484 (GRCm39) I484T possibly damaging Het
Plvap A G 8: 71,964,083 (GRCm39) V93A probably benign Het
Plxna4 T C 6: 32,142,697 (GRCm39) Y1586C probably damaging Het
Ppfia4 A T 1: 134,255,817 (GRCm39) L196Q possibly damaging Het
Ptpn13 T G 5: 103,665,335 (GRCm39) probably null Het
Ranbp17 T C 11: 33,169,223 (GRCm39) N997S probably benign Het
Rpap2 G T 5: 107,751,491 (GRCm39) probably null Het
Rrm1 T C 7: 102,116,131 (GRCm39) V683A probably benign Het
Ruvbl1 A G 6: 88,460,021 (GRCm39) probably null Het
Sh3pxd2a A G 19: 47,266,843 (GRCm39) Y277H probably damaging Het
Shank1 C T 7: 43,975,586 (GRCm39) P477S unknown Het
Shtn1 T C 19: 59,010,633 (GRCm39) E278G probably benign Het
Skap2 T A 6: 51,899,303 (GRCm39) I109F possibly damaging Het
Slc28a3 A C 13: 58,706,395 (GRCm39) I615M probably benign Het
Slc4a11 A G 2: 130,526,788 (GRCm39) L780P probably damaging Het
Slc5a4b T C 10: 75,917,301 (GRCm39) E245G probably benign Het
Slfn8 C T 11: 82,894,111 (GRCm39) A843T probably benign Het
Spidr T A 16: 15,958,610 (GRCm39) K51* probably null Het
Spopfm2 A T 3: 94,083,540 (GRCm39) Y90* probably null Het
Tas2r123 T C 6: 132,824,808 (GRCm39) V235A probably benign Het
Tgfbr3 T C 5: 107,278,335 (GRCm39) D757G probably benign Het
Tmem132d A T 5: 127,873,139 (GRCm39) V490D probably damaging Het
Top2a T A 11: 98,900,918 (GRCm39) H557L probably damaging Het
Trafd1 A G 5: 121,513,254 (GRCm39) I328T probably benign Het
Trappc11 G A 8: 47,972,700 (GRCm39) A291V probably damaging Het
Tuba1c A G 15: 98,935,835 (GRCm39) Y432C probably damaging Het
Utp11 T G 4: 124,577,043 (GRCm39) R109S possibly damaging Het
Vmn1r159 T G 7: 22,542,316 (GRCm39) T239P probably damaging Het
Vwce A T 19: 10,622,414 (GRCm39) N239Y probably damaging Het
Yes1 T C 5: 32,802,457 (GRCm39) probably null Het
Zfand6 A C 7: 84,265,030 (GRCm39) *224G probably null Het
Zfp408 A T 2: 91,475,450 (GRCm39) I668N probably damaging Het
Zfp647 TGCACG TGCACGCACG 15: 76,795,244 (GRCm39) probably null Het
Zfp946 T C 17: 22,674,418 (GRCm39) F391L probably damaging Het
Other mutations in Sncaip
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00504:Sncaip APN 18 53,018,035 (GRCm39) splice site probably null
IGL01554:Sncaip APN 18 53,002,006 (GRCm39) missense possibly damaging 0.94
IGL01802:Sncaip APN 18 53,002,109 (GRCm39) missense probably damaging 1.00
IGL02658:Sncaip APN 18 53,028,027 (GRCm39) missense possibly damaging 0.50
IGL02737:Sncaip APN 18 53,040,128 (GRCm39) missense probably benign 0.10
IGL03017:Sncaip APN 18 53,028,009 (GRCm39) missense possibly damaging 0.82
PIT4445001:Sncaip UTSW 18 53,002,016 (GRCm39) missense probably damaging 1.00
R0218:Sncaip UTSW 18 53,040,400 (GRCm39) missense probably benign 0.18
R0325:Sncaip UTSW 18 53,038,881 (GRCm39) missense probably damaging 1.00
R0450:Sncaip UTSW 18 53,001,781 (GRCm39) missense probably benign 0.08
R0469:Sncaip UTSW 18 53,001,781 (GRCm39) missense probably benign 0.08
R1494:Sncaip UTSW 18 53,001,958 (GRCm39) missense probably damaging 0.99
R1897:Sncaip UTSW 18 53,027,862 (GRCm39) splice site probably null
R1962:Sncaip UTSW 18 53,004,434 (GRCm39) missense probably damaging 1.00
R2238:Sncaip UTSW 18 53,001,619 (GRCm39) missense probably damaging 1.00
R2935:Sncaip UTSW 18 52,971,104 (GRCm39) missense probably damaging 1.00
R4044:Sncaip UTSW 18 53,040,475 (GRCm39) missense probably benign 0.01
R4694:Sncaip UTSW 18 53,039,629 (GRCm39) missense probably benign 0.00
R4810:Sncaip UTSW 18 53,040,271 (GRCm39) missense possibly damaging 0.47
R4850:Sncaip UTSW 18 53,004,456 (GRCm39) missense probably damaging 1.00
R4857:Sncaip UTSW 18 53,002,297 (GRCm39) missense probably benign 0.00
R5384:Sncaip UTSW 18 53,018,113 (GRCm39) missense probably damaging 1.00
R5610:Sncaip UTSW 18 53,001,991 (GRCm39) missense probably benign
R5645:Sncaip UTSW 18 53,028,028 (GRCm39) missense probably damaging 1.00
R5797:Sncaip UTSW 18 53,031,276 (GRCm39) missense probably benign 0.28
R5977:Sncaip UTSW 18 53,002,393 (GRCm39) missense probably benign
R6197:Sncaip UTSW 18 53,039,966 (GRCm39) missense probably damaging 1.00
R6369:Sncaip UTSW 18 53,001,676 (GRCm39) missense probably damaging 0.98
R6505:Sncaip UTSW 18 53,039,609 (GRCm39) nonsense probably null
R6604:Sncaip UTSW 18 53,038,918 (GRCm39) missense possibly damaging 0.71
R6880:Sncaip UTSW 18 53,002,136 (GRCm39) missense probably damaging 1.00
R7215:Sncaip UTSW 18 53,040,415 (GRCm39) nonsense probably null
R7234:Sncaip UTSW 18 53,048,416 (GRCm39) missense probably benign 0.00
R8523:Sncaip UTSW 18 52,971,088 (GRCm39) missense probably damaging 1.00
R8719:Sncaip UTSW 18 53,027,910 (GRCm39) missense probably damaging 1.00
R8781:Sncaip UTSW 18 53,039,614 (GRCm39) missense probably benign 0.00
R8786:Sncaip UTSW 18 53,031,334 (GRCm39) missense probably damaging 1.00
R8826:Sncaip UTSW 18 53,048,381 (GRCm39) missense probably benign
R8985:Sncaip UTSW 18 53,002,169 (GRCm39) missense probably benign 0.00
R9067:Sncaip UTSW 18 53,039,973 (GRCm39) missense probably damaging 1.00
R9187:Sncaip UTSW 18 53,040,011 (GRCm39) missense probably benign 0.22
R9632:Sncaip UTSW 18 53,039,726 (GRCm39) missense probably damaging 1.00
R9696:Sncaip UTSW 18 53,038,915 (GRCm39) missense probably damaging 1.00
Z1177:Sncaip UTSW 18 53,040,497 (GRCm39) missense possibly damaging 0.55
Predicted Primers PCR Primer
(F):5'- GCCCAGAAAGTTGCCACAAG -3'
(R):5'- CACTCTCTAGATAGCACTCACTG -3'

Sequencing Primer
(F):5'- GTTGCCACAAGCCCCAAGAG -3'
(R):5'- GGGCTCACAGGATTTCCCTTG -3'
Posted On 2016-04-27