Mutagenetix > Incidental Mutation

Incidental Mutation 'R0469:Sncaip'

43177

Institutional Source

Beutler Lab

Gene Symbol

Sncaip

Ensembl Gene

ENSMUSG00000024534

Gene Name

synuclein, alpha interacting protein (synphilin)

Synonyms

synphilin-1, SYPH1, 4933427B05Rik

MMRRC Submission

038669-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.193) question?

Stock #

R0469 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

52900872-53049007 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 53001781 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 101 (T101A)

Ref Sequence

ENSEMBL: ENSMUSP00000111069 (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 benign
Transcript: ENSMUST00000025413
AA Change: T101A

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000025413
Gene: ENSMUSG00000024534
AA Change: T101A

Domain	Start	End	E-Value	Type
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: T101A

PolyPhen 2 Score 0.077 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000111069
Gene: ENSMUSG00000024534
AA Change: T101A

Domain	Start	End	E-Value	Type
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: T101A

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000127189
Gene: ENSMUSG00000024534
AA Change: T101A

Domain	Start	End	E-Value	Type
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: T101A

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000137549
Gene: ENSMUSG00000024534
AA Change: T101A

Domain	Start	End	E-Value	Type
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: ENSMUST00000178678
AA Change: T101A

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000137367
Gene: ENSMUSG00000024534
AA Change: T101A

Domain	Start	End	E-Value	Type
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

probably benign
Transcript: ENSMUST00000179625
AA Change: T101A

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000136838
Gene: ENSMUSG00000024534
AA Change: T101A

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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: 99.0%
3x: 98.2%
10x: 96.2%
20x: 92.3%

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcg3	A	G	5: 105,125,482 (GRCm39)	I67T	probably damaging	Het
Acoxl	G	A	2: 127,722,423 (GRCm39)		probably null	Het
Adam10	T	A	9: 70,655,530 (GRCm39)	W333R	probably damaging	Het
Ahnak	C	T	19: 8,995,596 (GRCm39)	R5627*	probably null	Het
Alms1	A	T	6: 85,597,351 (GRCm39)	R1195*	probably null	Het
Arih2	T	A	9: 108,482,291 (GRCm39)	H490L	possibly damaging	Het
Arpc1b	T	A	5: 145,064,525 (GRCm39)	W361R	probably damaging	Het
B3gntl1	A	T	11: 121,563,851 (GRCm39)	V3D	probably benign	Het
Baiap2l1	T	C	5: 144,212,701 (GRCm39)	Y438C	probably damaging	Het
Bicc1	C	A	10: 70,915,045 (GRCm39)	R73L	probably benign	Het
Ccdc110	T	A	8: 46,388,194 (GRCm39)	N50K	probably benign	Het
Ccdc168	T	A	1: 44,100,257 (GRCm39)	K280N	possibly damaging	Het
Cep76	A	T	18: 67,767,850 (GRCm39)	N227K	probably benign	Het
Col6a4	A	T	9: 105,957,746 (GRCm39)	V26D	probably damaging	Het
Cpe	T	A	8: 65,064,501 (GRCm39)	I233F	probably damaging	Het
Cpsf2	T	C	12: 101,955,045 (GRCm39)	V272A	probably damaging	Het
Defa34	A	G	8: 22,155,988 (GRCm39)		probably null	Het
Dnah12	A	G	14: 26,520,856 (GRCm39)	R1892G	probably damaging	Het
Efr3b	G	T	12: 4,032,058 (GRCm39)	D183E	probably benign	Het
Epyc	A	G	10: 97,485,625 (GRCm39)	T22A	probably benign	Het
Fam83a	C	A	15: 57,873,322 (GRCm39)	Q384K	probably benign	Het
Fam83b	G	T	9: 76,400,108 (GRCm39)	L332I	possibly damaging	Het
Ggn	C	T	7: 28,870,721 (GRCm39)	P47S	probably damaging	Het
Gli3	T	G	13: 15,899,370 (GRCm39)	L919R	probably damaging	Het
Golgb1	A	G	16: 36,751,997 (GRCm39)	I3144V	probably benign	Het
Gpr108	T	C	17: 57,542,358 (GRCm39)	D549G	possibly damaging	Het
Gpr39	C	T	1: 125,605,237 (GRCm39)	T55M	probably damaging	Het
Grk4	A	G	5: 34,873,557 (GRCm39)	T208A	probably damaging	Het
Gucy2e	T	C	11: 69,126,402 (GRCm39)	D326G	probably benign	Het
H2-Eb2	C	T	17: 34,553,218 (GRCm39)	Q135*	probably null	Het
Hectd4	T	A	5: 121,419,959 (GRCm39)	Y635N	possibly damaging	Het
Hectd4	G	A	5: 121,443,736 (GRCm39)	E1319K	possibly damaging	Het
Hnrnph3	T	A	10: 62,853,994 (GRCm39)	R41S	probably benign	Het
Hnrnph3	T	A	10: 62,855,279 (GRCm39)	D2V	probably damaging	Het
Hs3st2	T	C	7: 121,099,792 (GRCm39)	S213P	probably damaging	Het
Ikbkb	A	T	8: 23,161,651 (GRCm39)	C412*	probably null	Het
Kctd21	T	C	7: 96,996,748 (GRCm39)	F74L	probably damaging	Het
Krt23	T	A	11: 99,377,608 (GRCm39)	I133L	probably damaging	Het
Krt74	T	C	15: 101,671,751 (GRCm39)		noncoding transcript	Het
Lmtk3	T	A	7: 45,443,536 (GRCm39)	L740M	possibly damaging	Het
Lrrc10	T	A	10: 116,881,695 (GRCm39)	L123Q	probably damaging	Het
Map1a	A	T	2: 121,136,255 (GRCm39)	H2357L	probably benign	Het
Mcf2l	A	G	8: 13,047,337 (GRCm39)	D233G	probably damaging	Het
Mdn1	A	G	4: 32,738,619 (GRCm39)	N3524S	probably benign	Het
Msto1	A	G	3: 88,818,848 (GRCm39)	L269P	probably benign	Het
Naca	C	T	10: 127,880,659 (GRCm39)	A1897V	probably benign	Het
Or1j10	A	T	2: 36,267,474 (GRCm39)	I229F	probably benign	Het
Or4a39	A	T	2: 89,237,135 (GRCm39)	M96K	probably damaging	Het
Or5w15	A	G	2: 87,567,825 (GRCm39)	V281A	probably damaging	Het
Or8b12i	T	C	9: 20,082,561 (GRCm39)	Y102C	probably benign	Het
Pdzrn3	A	T	6: 101,128,014 (GRCm39)	I884N	probably damaging	Het
Phf24	G	T	4: 42,933,761 (GRCm39)	V48L	possibly damaging	Het
Pkn1	C	A	8: 84,398,953 (GRCm39)	C678F	probably damaging	Het
Pla2g4a	T	A	1: 149,716,398 (GRCm39)	M688L	possibly damaging	Het
Ppp1r3c	A	T	19: 36,711,617 (GRCm39)	F51Y	possibly damaging	Het
Psen2	T	C	1: 180,066,479 (GRCm39)	T153A	probably damaging	Het
Rbmx	C	T	X: 56,436,926 (GRCm39)		probably null	Het
Rbp3	A	G	14: 33,684,376 (GRCm39)	K1135R	possibly damaging	Het
Slco2b1	T	A	7: 99,310,743 (GRCm39)	M603L	probably benign	Het
Ssh1	A	T	5: 114,084,766 (GRCm39)	D448E	probably benign	Het
Ssmem1	A	T	6: 30,519,547 (GRCm39)		probably null	Het
Stk11	T	C	10: 79,961,920 (GRCm39)	V47A	probably damaging	Het
Sv2b	T	G	7: 74,786,140 (GRCm39)	M427L	probably benign	Het
Syne1	A	G	10: 5,317,600 (GRCm39)	L498P	probably damaging	Het
Syne2	T	C	12: 75,900,923 (GRCm39)		probably null	Het
Taf6l	G	T	19: 8,755,885 (GRCm39)	H254Q	probably benign	Het
Tas2r123	T	C	6: 132,824,295 (GRCm39)	V64A	probably benign	Het
Tm9sf1	A	T	14: 55,878,886 (GRCm39)	F169I	possibly damaging	Het
Tmpo	A	C	10: 90,998,958 (GRCm39)	I276M	probably benign	Het
Tnnc1	A	G	14: 30,933,365 (GRCm39)	D149G	probably damaging	Het
Tpr	AAGAGAGAGAGAGAG	AAGAGAGAGAGAG	1: 150,299,418 (GRCm39)		probably null	Het
Traf3ip3	T	A	1: 192,860,539 (GRCm39)		probably null	Het
Trim55	G	T	3: 19,725,256 (GRCm39)	V258L	possibly damaging	Het
Trpm1	G	A	7: 63,873,506 (GRCm39)	G587D	probably damaging	Het
Ttn	A	G	2: 76,560,756 (GRCm39)	V29215A	probably damaging	Het
Ube2u	A	G	4: 100,343,870 (GRCm39)	I90V	probably benign	Het
Upb1	T	C	10: 75,250,917 (GRCm39)		probably null	Het
Vmn2r57	A	T	7: 41,077,216 (GRCm39)	S317T	possibly damaging	Het
Wdr73	G	A	7: 80,547,698 (GRCm39)	Q107*	probably null	Het
Zfp628	A	T	7: 4,922,732 (GRCm39)	Q318L	probably benign	Het

Other mutations in Sncaip

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- GGCTGGAATTGTGGTGTCTCAACTC -3'
(R):5'- ATGCAGGGCCACATTTACCCAGAG -3'

Sequencing Primer
(F):5'- GTGGTGTCTCAACTCTCATTACAAAC -3'
(R):5'- ATTTACCCAGAGCTGGCGAG -3'

Posted On

2013-05-23