Incidental Mutation 'PIT4445001:Sncaip'
ID 555441
Institutional Source Beutler Lab
Gene Symbol Sncaip
Ensembl Gene ENSMUSG00000024534
Gene Name synuclein, alpha interacting protein (synphilin)
Synonyms synphilin-1, SYPH1, 4933427B05Rik
Accession Numbers
Essential gene? Probably non essential (E-score: 0.193) question?
Stock # PIT4445001 (G1)
Quality Score 156.008
Status Not validated
Chromosome 18
Chromosomal Location 52900872-53049007 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 53002016 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Serine at position 179 (L179S)
Ref Sequence ENSEMBL: ENSMUSP00000025413 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025413] [ENSMUST00000115410] [ENSMUST00000163742] [ENSMUST00000177861] [ENSMUST00000178011] [ENSMUST00000178678] [ENSMUST00000178883] [ENSMUST00000179625] [ENSMUST00000179689] [ENSMUST00000180259]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000025413
AA Change: L179S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000025413
Gene: ENSMUSG00000024534
AA Change: L179S

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 damaging
Transcript: ENSMUST00000115410
AA Change: L179S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000111069
Gene: ENSMUSG00000024534
AA Change: L179S

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 damaging
Transcript: ENSMUST00000163742
AA Change: L179S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000127189
Gene: ENSMUSG00000024534
AA Change: L179S

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 damaging
Transcript: ENSMUST00000178011
AA Change: L179S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000137549
Gene: ENSMUSG00000024534
AA Change: L179S

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 damaging
Transcript: ENSMUST00000178678
AA Change: L179S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000137367
Gene: ENSMUSG00000024534
AA Change: L179S

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: ENSMUST00000178883
Predicted Effect possibly damaging
Transcript: ENSMUST00000179625
AA Change: L179S

PolyPhen 2 Score 0.811 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000136838
Gene: ENSMUSG00000024534
AA Change: L179S

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: ENSMUST00000179689
SMART Domains Protein: ENSMUSP00000137107
Gene: ENSMUSG00000024534

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: ENSMUST00000180259
Coding Region Coverage
  • 1x: 93.5%
  • 3x: 90.8%
  • 10x: 84.5%
  • 20x: 70.9%
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8a T C 11: 109,966,377 (GRCm39) K419E probably damaging Het
Adam7 T A 14: 68,747,197 (GRCm39) K587N possibly damaging Het
Agl T C 3: 116,565,109 (GRCm39) M382V Het
Agpat3 A T 10: 78,109,927 (GRCm39) F341I possibly damaging Het
Ampd2 A T 3: 107,982,328 (GRCm39) L767Q probably damaging Het
Arhgap28 A T 17: 68,203,230 (GRCm39) D124E possibly damaging Het
Arhgap32 T C 9: 32,172,152 (GRCm39) L1644P probably damaging Het
Asic4 T C 1: 75,427,771 (GRCm39) V99A probably benign Het
Asns T A 6: 7,689,277 (GRCm39) N75I probably damaging Het
Atp10a A G 7: 58,453,215 (GRCm39) D798G probably damaging Het
Atp8a1 A G 5: 67,780,003 (GRCm39) V1145A Het
Ccdc171 A G 4: 83,579,984 (GRCm39) Q577R probably damaging Het
Cd247 T A 1: 165,688,605 (GRCm39) D154E probably damaging Het
Ceacam1 A T 7: 25,175,881 (GRCm39) N104K probably damaging Het
Chfr A G 5: 110,299,543 (GRCm39) D312G possibly damaging Het
Ddb1 C A 19: 10,603,334 (GRCm39) L881I probably damaging Het
Dgkh A T 14: 78,813,382 (GRCm39) I1032N possibly damaging Het
Efcab6 A T 15: 83,788,468 (GRCm39) V942D probably benign Het
Fmo5 A G 3: 97,558,844 (GRCm39) T435A probably benign Het
Fpr1 T C 17: 18,097,155 (GRCm39) Q278R probably benign Het
Fzr1 C T 10: 81,205,228 (GRCm39) W256* probably null Het
Gabrb1 T C 5: 72,266,125 (GRCm39) S261P probably damaging Het
Galr2 G T 11: 116,172,474 (GRCm39) A55S probably benign Het
Gbp2 A T 3: 142,343,227 (GRCm39) K581N probably benign Het
Gria1 A T 11: 57,076,664 (GRCm39) Y89F probably damaging Het
Ibsp T A 5: 104,450,170 (GRCm39) I26N possibly damaging Het
Igf1r T C 7: 67,857,211 (GRCm39) F1058L probably damaging Het
Ighv1-16 A C 12: 114,629,680 (GRCm39) C36G probably benign Het
Igll1 T C 16: 16,678,783 (GRCm39) T176A probably benign Het
Ilkap T C 1: 91,313,067 (GRCm39) T143A probably benign Het
Kdm3b A T 18: 34,926,168 (GRCm39) K103* probably null Het
Mphosph9 A G 5: 124,436,853 (GRCm39) I497T possibly damaging Het
Mrgpra3 G A 7: 47,239,908 (GRCm39) T6I possibly damaging Het
Mrpl38 T C 11: 116,023,384 (GRCm39) probably null Het
Myo3a A T 2: 22,434,457 (GRCm39) E813V possibly damaging Het
Myo7b T C 18: 32,095,405 (GRCm39) K1851R probably damaging Het
Myo7b G T 18: 32,092,519 (GRCm39) Q2093K possibly damaging Het
P3h2 T A 16: 25,803,749 (GRCm39) D339V probably benign Het
Pcdhb6 C A 18: 37,468,300 (GRCm39) P407Q possibly damaging Het
Plch2 C A 4: 155,093,483 (GRCm39) R153L probably damaging Het
Plppr4 G A 3: 117,153,957 (GRCm39) probably benign Het
Ppp1r3a A G 6: 14,717,776 (GRCm39) F1046S probably damaging Het
Pramel41 T G 5: 94,596,366 (GRCm39) W468G probably benign Het
Prkacb A T 3: 146,461,446 (GRCm39) L107M probably benign Het
Ranbp17 A G 11: 33,431,020 (GRCm39) probably null Het
Rasl11b C A 5: 74,357,994 (GRCm39) P88Q probably damaging Het
Rcc2 A G 4: 140,448,460 (GRCm39) E503G possibly damaging Het
Rnf216 T A 5: 143,071,758 (GRCm39) K407N probably damaging Het
Rusf1 A G 7: 127,875,706 (GRCm39) V243A probably benign Het
Scrn3 G A 2: 73,148,673 (GRCm39) M81I possibly damaging Het
Scube2 T C 7: 109,408,387 (GRCm39) T687A probably benign Het
Serpinb10 T A 1: 107,463,728 (GRCm39) F3L probably benign Het
Sgcb C T 5: 73,797,155 (GRCm39) V202I probably damaging Het
Sgce A G 6: 4,689,654 (GRCm39) V429A possibly damaging Het
Sh3rf2 T C 18: 42,286,229 (GRCm39) V574A probably benign Het
Sntg2 A T 12: 30,362,571 (GRCm39) D58E probably damaging Het
Taar3 T C 10: 23,825,586 (GRCm39) I44T possibly damaging Het
Tmem87b G A 2: 128,673,391 (GRCm39) V227I probably benign Het
Tnfsf9 T C 17: 57,412,517 (GRCm39) L29P possibly damaging Het
Tnip2 T C 5: 34,654,215 (GRCm39) H391R probably benign Het
Traf5 A G 1: 191,729,768 (GRCm39) Y125H Het
Ttc23 T G 7: 67,316,961 (GRCm39) I77M probably damaging Het
Ube2l3 T C 16: 16,978,036 (GRCm39) N43S probably benign Het
Vars2 A T 17: 35,977,103 (GRCm39) C142* probably null Het
Vmn2r15 A C 5: 109,435,008 (GRCm39) D565E probably damaging Het
Vmn2r56 C T 7: 12,449,153 (GRCm39) probably null Het
Vmn2r79 A T 7: 86,651,408 (GRCm39) D269V possibly damaging Het
Vmn2r85 A T 10: 130,261,572 (GRCm39) M255K probably benign Het
Wfdc6a T A 2: 164,421,746 (GRCm39) *137C probably null Het
Wipi2 T C 5: 142,652,639 (GRCm39) V417A probably benign Het
Xirp2 G T 2: 67,340,116 (GRCm39) V786L possibly damaging Het
Zdhhc13 G A 7: 48,445,697 (GRCm39) G26S probably benign Het
Zscan25 T A 5: 145,227,422 (GRCm39) V362D 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
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
R4939:Sncaip UTSW 18 53,040,335 (GRCm39) missense possibly damaging 0.53
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'- CGGAGACTCTGGAGAACAAC -3'
(R):5'- TCTCGGAGTCTTCTGTAGAGAG -3'

Sequencing Primer
(F):5'- CTCAGCCCTGAAGATGGAGTC -3'
(R):5'- AGTCTTCTGTAGAGAGCTTGTGC -3'
Posted On 2019-06-07