Mutagenetix > Incidental Mutation

Incidental Mutation 'R0601:Sytl2'

55398

Institutional Source

Beutler Lab

Gene Symbol

Sytl2

Ensembl Gene

ENSMUSG00000030616

Gene Name

synaptotagmin-like 2

Synonyms

Slp2-b, Slp2-c, Slp2-d, Slp2, Slp2-a

MMRRC Submission

038790-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.384) question?

Stock #

R0601 (G1)

Quality Score

138

Status

Validated

Chromosome

Chromosomal Location

89951460-90059927 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 90044374 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Asparagine at position 572 (D572N)

Ref Sequence

ENSEMBL: ENSMUSP00000102829 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000107210] [ENSMUST00000107211] [ENSMUST00000190731] [ENSMUST00000190837]

AlphaFold

Q99N50

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000098310

SMART Domains

Protein: ENSMUSP00000095912
Gene: ENSMUSG00000030616

Domain	Start	End	E-Value	Type
low complexity region	938	966	N/A	INTRINSIC
C2	990	1095	4.59e-15	SMART
C2	1139	1242	6.44e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000107210

SMART Domains

Protein: ENSMUSP00000102828
Gene: ENSMUSG00000030616

Domain	Start	End	E-Value	Type
Pfam:FYVE_2	5	59	5.5e-9	PFAM
low complexity region	192	205	N/A	INTRINSIC
low complexity region	317	328	N/A	INTRINSIC
C2	620	725	4.59e-15	SMART
C2	769	872	6.44e-10	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000107211
AA Change: D572N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000102829
Gene: ENSMUSG00000030616
AA Change: D572N

Domain	Start	End	E-Value	Type
Pfam:FYVE_2	5	59	5.6e-9	PFAM
low complexity region	192	205	N/A	INTRINSIC
low complexity region	317	328	N/A	INTRINSIC
low complexity region	592	620	N/A	INTRINSIC
C2	644	749	4.59e-15	SMART
C2	793	896	6.44e-10	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189194

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000190365

Predicted Effect

possibly damaging
Transcript: ENSMUST00000190731
AA Change: D588N

PolyPhen 2 Score 0.635 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000139865
Gene: ENSMUSG00000030616
AA Change: D588N

Domain	Start	End	E-Value	Type
Pfam:FYVE_2	5	59	5.8e-9	PFAM
low complexity region	192	205	N/A	INTRINSIC
low complexity region	317	328	N/A	INTRINSIC
low complexity region	608	636	N/A	INTRINSIC
C2	660	765	4.59e-15	SMART
C2	809	912	6.44e-10	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000190837
AA Change: D561N

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139450
Gene: ENSMUSG00000030616
AA Change: D561N

Domain	Start	End	E-Value	Type
Pfam:FYVE_2	5	59	5.6e-9	PFAM
low complexity region	82	93	N/A	INTRINSIC
low complexity region	165	178	N/A	INTRINSIC
low complexity region	290	301	N/A	INTRINSIC
low complexity region	581	609	N/A	INTRINSIC
C2	633	738	4.59e-15	SMART
C2	782	885	6.44e-10	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208809

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208486

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209188

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207928

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208580

Meta Mutation Damage Score

0.1539

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.6%
20x: 95.2%

Validation Efficiency

98% (119/122)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a synaptotagmin-like protein (SLP) that belongs to a C2 domain-containing protein family. The SLP homology domain (SHD) of this protein has been shown to specifically bind the GTP-bound form of Ras-related protein Rab-27A (RAB27A). This protein plays a role in RAB27A-dependent vesicle trafficking and controls melanosome distribution in the cell periphery. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Jun 2009]
PHENOTYPE: Mice homozygous for a null allele display abnormal gastric surface mucus cell morphology and reduced basal mucin secretion from gastric cells [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 119 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930596D02Rik	T	G	14: 35,532,146 (GRCm39)	D143A	probably damaging	Het
Abca9	C	T	11: 110,007,884 (GRCm39)		probably null	Het
Abcc5	A	G	16: 20,223,309 (GRCm39)		probably benign	Het
Ablim3	T	A	18: 61,982,441 (GRCm39)	D168V	probably benign	Het
Acsl3	C	T	1: 78,673,896 (GRCm39)	S352F	probably damaging	Het
Adgrl4	A	T	3: 151,204,066 (GRCm39)		probably benign	Het
Arhgap29	A	G	3: 121,784,759 (GRCm39)	K229E	probably damaging	Het
Atad3a	A	T	4: 155,831,864 (GRCm39)	V470D	probably damaging	Het
Atp8b1	A	G	18: 64,704,724 (GRCm39)		probably null	Het
Bcl2	G	A	1: 106,640,292 (GRCm39)	R107C	probably damaging	Het
Bpifa5	A	G	2: 154,006,175 (GRCm39)	N121S	possibly damaging	Het
Bpifb4	G	A	2: 153,789,203 (GRCm39)		probably benign	Het
Bptf	T	A	11: 106,952,518 (GRCm39)	T2112S	probably benign	Het
Btnl4	T	C	17: 34,688,285 (GRCm39)	K498E	probably benign	Het
Calhm2	A	G	19: 47,129,469 (GRCm39)		probably null	Het
Capn3	A	T	2: 120,333,077 (GRCm39)		probably null	Het
Caps2	T	C	10: 112,031,695 (GRCm39)	F265L	possibly damaging	Het
Casp3	G	T	8: 47,089,262 (GRCm39)	C170F	probably benign	Het
Ccdc39	T	C	3: 33,873,988 (GRCm39)	R615G	probably damaging	Het
Cd177	A	G	7: 24,451,738 (GRCm39)	I426T	probably benign	Het
Cfap53	G	A	18: 74,433,221 (GRCm39)	R102H	possibly damaging	Het
Cfhr3	G	A	1: 139,521,623 (GRCm39)		noncoding transcript	Het
Col7a1	T	C	9: 108,809,652 (GRCm39)		probably benign	Het
Cplx3	T	C	9: 57,513,357 (GRCm39)	E24G	possibly damaging	Het
Dhx30	A	G	9: 109,915,782 (GRCm39)		probably null	Het
Dnah8	T	A	17: 30,927,332 (GRCm39)	N1329K	probably benign	Het
Dnajc11	C	G	4: 152,054,393 (GRCm39)	R200G	probably damaging	Het
Dok3	A	T	13: 55,672,076 (GRCm39)	F201I	probably benign	Het
Dpf2	A	T	19: 5,952,240 (GRCm39)	H303Q	probably damaging	Het
Dtnb	A	G	12: 3,785,039 (GRCm39)		probably benign	Het
Dync2i1	T	C	12: 116,219,555 (GRCm39)	D129G	possibly damaging	Het
Elk3	T	C	10: 93,101,343 (GRCm39)	E136G	probably damaging	Het
Ephb1	T	C	9: 102,072,329 (GRCm39)	D150G	probably damaging	Het
Erbb3	A	G	10: 128,412,881 (GRCm39)	S570P	probably benign	Het
F2	A	T	2: 91,463,656 (GRCm39)		probably null	Het
Fanca	A	T	8: 124,035,252 (GRCm39)	M231K	probably damaging	Het
Fbxo34	T	C	14: 47,767,714 (GRCm39)	V358A	probably benign	Het
Foxp1	C	T	6: 98,907,083 (GRCm39)	E666K	probably damaging	Het
Fto	A	G	8: 92,128,430 (GRCm39)		probably null	Het
Gbp2	C	T	3: 142,336,519 (GRCm39)	R290C	possibly damaging	Het
Gm57859	T	A	11: 113,578,712 (GRCm39)	S36T	probably benign	Het
Grik2	T	G	10: 49,298,693 (GRCm39)	S343R	probably damaging	Het
Heatr5b	A	T	17: 79,075,974 (GRCm39)	M1448K	probably benign	Het
Hmgn3	A	T	9: 83,028,482 (GRCm39)		probably null	Het
Htt	T	C	5: 35,003,347 (GRCm39)	V1274A	probably benign	Het
Kcnh8	A	G	17: 53,201,033 (GRCm39)	D489G	probably damaging	Het
Kcnip3	A	T	2: 127,300,317 (GRCm39)		probably benign	Het
Kdm5a	A	G	6: 120,379,632 (GRCm39)	T647A	possibly damaging	Het
Krt72	T	C	15: 101,694,491 (GRCm39)	R135G	probably damaging	Het
Larp7	T	A	3: 127,337,858 (GRCm39)	K400N	probably damaging	Het
Lifr	T	C	15: 7,198,753 (GRCm39)		probably null	Het
Lima1	G	A	15: 99,678,353 (GRCm39)	P696L	probably damaging	Het
Lrrc8e	T	G	8: 4,285,239 (GRCm39)		probably null	Het
Map1a	A	G	2: 121,129,083 (GRCm39)	R116G	probably damaging	Het
Map3k13	A	G	16: 21,723,999 (GRCm39)	E327G	possibly damaging	Het
Med13	A	G	11: 86,236,788 (GRCm39)	V123A	possibly damaging	Het
Megf8	A	C	7: 25,027,965 (GRCm39)	H205P	probably benign	Het
Met	G	A	6: 17,555,631 (GRCm39)		probably null	Het
Mfsd14b	A	C	13: 65,234,964 (GRCm39)	V71G	possibly damaging	Het
Mpl	T	A	4: 118,300,733 (GRCm39)	T599S	probably benign	Het
Myh15	A	T	16: 48,881,944 (GRCm39)	D62V	probably damaging	Het
Myo5a	A	G	9: 75,081,297 (GRCm39)	T961A	probably benign	Het
Myrfl	A	G	10: 116,612,665 (GRCm39)	Y895H	probably damaging	Het
Nap1l1	T	C	10: 111,326,224 (GRCm39)		probably benign	Het
Ncapd3	T	A	9: 26,952,803 (GRCm39)	Y111N	probably benign	Het
Nlrc3	A	G	16: 3,766,113 (GRCm39)		probably benign	Het
Nsun2	G	T	13: 69,781,361 (GRCm39)	V657L	probably benign	Het
Or10g1b	C	A	14: 52,627,283 (GRCm39)	G316*	probably null	Het
Or4a74	T	A	2: 89,439,564 (GRCm39)	N294I	probably benign	Het
Or4b13	T	C	2: 90,083,278 (GRCm39)	D18G	probably benign	Het
Or52d1	A	T	7: 103,756,349 (GRCm39)	I288F	possibly damaging	Het
Or52e19	T	C	7: 102,959,371 (GRCm39)	S148P	probably damaging	Het
Or5k3	G	A	16: 58,970,117 (GRCm39)	M301I	probably benign	Het
Or5m13b	A	T	2: 85,753,722 (GRCm39)	I37F	probably benign	Het
Or6c68	T	A	10: 129,157,885 (GRCm39)	M131K	possibly damaging	Het
Osbpl3	A	T	6: 50,276,383 (GRCm39)	V795D	probably benign	Het
Osbpl5	T	C	7: 143,263,286 (GRCm39)	D155G	probably damaging	Het
Parm1	G	A	5: 91,742,123 (GRCm39)	V164I	probably benign	Het
Pgd	A	T	4: 149,241,267 (GRCm39)		probably benign	Het
Pkp1	G	A	1: 135,805,920 (GRCm39)	R593W	probably damaging	Het
Polr2l	A	T	7: 141,053,255 (GRCm39)	V53E	probably damaging	Het
Ppp4c	G	T	7: 126,386,460 (GRCm39)	T29K	probably benign	Het
Ppp4r4	T	A	12: 103,566,779 (GRCm39)		probably benign	Het
Ptprd	A	G	4: 76,018,711 (GRCm39)	S688P	probably benign	Het
Rab3b	A	T	4: 108,747,586 (GRCm39)	I28F	probably damaging	Het
Rnase4	T	C	14: 51,342,552 (GRCm39)	L92P	probably benign	Het
Rnpc3	T	C	3: 113,413,755 (GRCm39)	E229G	probably benign	Het
Rtraf	A	T	14: 19,866,274 (GRCm39)	D147E	possibly damaging	Het
Rttn	G	A	18: 89,061,090 (GRCm39)	G1086D	probably benign	Het
Ryr2	A	G	13: 11,720,519 (GRCm39)		probably null	Het
Sft2d2	T	C	1: 165,011,430 (GRCm39)	I126V	probably benign	Het
Skap1	G	T	11: 96,614,236 (GRCm39)		probably benign	Het
Slc14a2	A	T	18: 78,200,394 (GRCm39)	L753*	probably null	Het
Slc25a5	G	A	X: 36,059,408 (GRCm39)	A9T	probably benign	Het
Slc30a5	T	C	13: 100,951,278 (GRCm39)		probably benign	Het
Slc5a4b	A	C	10: 75,899,870 (GRCm39)	I456S	possibly damaging	Het
Slc9a4	A	T	1: 40,642,230 (GRCm39)	S400C	probably damaging	Het
Slx1b	T	A	7: 126,291,812 (GRCm39)	H84L	probably damaging	Het
Sptbn1	T	C	11: 30,100,008 (GRCm39)	Y190C	probably damaging	Het
Stk32b	T	C	5: 37,688,910 (GRCm39)	Q138R	probably damaging	Het
Syt6	C	A	3: 103,528,206 (GRCm39)	D308E	probably damaging	Het
Taok2	A	T	7: 126,478,605 (GRCm39)	L109Q	probably damaging	Het
Tbl1xr1	T	C	3: 22,233,483 (GRCm39)		probably benign	Het
Tlk1	A	G	2: 70,544,502 (GRCm39)	I711T	probably benign	Het
Trf	A	G	9: 103,100,132 (GRCm39)		probably null	Het
Trpc2	A	G	7: 101,733,572 (GRCm39)	T548A	possibly damaging	Het
Ttbk2	A	T	2: 120,655,777 (GRCm39)	I29N	possibly damaging	Het
Tti1	A	T	2: 157,835,292 (GRCm39)	C989S	probably damaging	Het
Txndc8	A	G	4: 58,000,256 (GRCm39)	Y108H	probably benign	Het
Ugt2b1	A	T	5: 87,065,539 (GRCm39)	V500D	possibly damaging	Het
Vmn1r34	A	G	6: 66,614,648 (GRCm39)	I30T	possibly damaging	Het
Vmn2r115	A	G	17: 23,579,074 (GRCm39)	K849R	probably null	Het
Vmn2r76	T	A	7: 85,875,323 (GRCm39)		probably null	Het
Vps13c	T	A	9: 67,834,754 (GRCm39)	S1694R	probably benign	Het
Wdfy3	G	T	5: 101,984,038 (GRCm39)	P3509T	probably benign	Het
Wdr59	GGGTGGTG	GGGTG	8: 112,207,172 (GRCm39)		probably benign	Het
Wnt8b	T	A	19: 44,482,106 (GRCm39)	W40R	probably benign	Het
Xrra1	A	G	7: 99,560,175 (GRCm39)	I384V	possibly damaging	Het
Zfp11	A	T	5: 129,734,971 (GRCm39)	H163Q	probably damaging	Het

Other mutations in Sytl2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00516:Sytl2	APN	7	90,022,113 (GRCm39)	missense	probably benign	0.25
IGL00657:Sytl2	APN	7	90,050,618 (GRCm39)	missense	probably benign	0.40
IGL00788:Sytl2	APN	7	90,031,906 (GRCm39)	intron	probably benign
IGL00834:Sytl2	APN	7	90,031,844 (GRCm39)	intron	probably benign
IGL01833:Sytl2	APN	7	90,045,745 (GRCm39)	missense	probably damaging	0.99
IGL01866:Sytl2	APN	7	90,031,047 (GRCm39)	intron	probably benign
IGL02215:Sytl2	APN	7	90,030,422 (GRCm39)	intron	probably benign
IGL02934:Sytl2	APN	7	90,025,200 (GRCm39)	missense	probably benign	0.00
IGL03095:Sytl2	APN	7	90,041,642 (GRCm39)	missense	probably damaging	1.00
finder	UTSW	7	90,024,860 (GRCm39)	missense	probably damaging	1.00
keeper	UTSW	7	90,007,432 (GRCm39)	nonsense	probably null
R0126:Sytl2	UTSW	7	90,045,797 (GRCm39)	missense	probably damaging	1.00
R0269:Sytl2	UTSW	7	90,052,228 (GRCm39)	splice site	probably benign
R0270:Sytl2	UTSW	7	90,052,228 (GRCm39)	splice site	probably benign
R0271:Sytl2	UTSW	7	90,052,228 (GRCm39)	splice site	probably benign
R0288:Sytl2	UTSW	7	90,052,228 (GRCm39)	splice site	probably benign
R0528:Sytl2	UTSW	7	90,052,228 (GRCm39)	splice site	probably benign
R0610:Sytl2	UTSW	7	90,030,061 (GRCm39)	intron	probably benign
R1634:Sytl2	UTSW	7	90,044,390 (GRCm39)	missense	probably damaging	1.00
R1777:Sytl2	UTSW	7	90,052,260 (GRCm39)	missense	probably benign	0.25
R2040:Sytl2	UTSW	7	90,031,069 (GRCm39)	intron	probably benign
R3788:Sytl2	UTSW	7	90,025,289 (GRCm39)	missense	probably benign	0.00
R3843:Sytl2	UTSW	7	90,009,367 (GRCm39)	missense	possibly damaging	0.77
R3952:Sytl2	UTSW	7	90,030,700 (GRCm39)	intron	probably benign
R4082:Sytl2	UTSW	7	90,057,635 (GRCm39)	missense	possibly damaging	0.88
R4600:Sytl2	UTSW	7	90,024,977 (GRCm39)	missense	probably benign	0.11
R4651:Sytl2	UTSW	7	90,024,633 (GRCm39)	missense	probably damaging	1.00
R4724:Sytl2	UTSW	7	89,998,000 (GRCm39)	start codon destroyed	probably null	1.00
R4730:Sytl2	UTSW	7	90,030,457 (GRCm39)	intron	probably benign
R4870:Sytl2	UTSW	7	90,038,106 (GRCm39)	missense	probably damaging	1.00
R4959:Sytl2	UTSW	7	90,025,245 (GRCm39)	missense	probably damaging	0.97
R4995:Sytl2	UTSW	7	90,031,465 (GRCm39)	intron	probably benign
R5009:Sytl2	UTSW	7	90,030,523 (GRCm39)	intron	probably benign
R5096:Sytl2	UTSW	7	90,025,290 (GRCm39)	missense	possibly damaging	0.49
R5191:Sytl2	UTSW	7	90,024,860 (GRCm39)	missense	probably damaging	1.00
R5305:Sytl2	UTSW	7	90,031,071 (GRCm39)	intron	probably benign
R5538:Sytl2	UTSW	7	90,038,114 (GRCm39)	missense	probably benign	0.03
R5792:Sytl2	UTSW	7	90,024,897 (GRCm39)	missense	probably damaging	0.98
R6378:Sytl2	UTSW	7	90,007,432 (GRCm39)	nonsense	probably null
R6982:Sytl2	UTSW	7	90,045,772 (GRCm39)	missense	probably damaging	0.96
R7456:Sytl2	UTSW	7	89,998,055 (GRCm39)	missense	probably damaging	1.00
R7600:Sytl2	UTSW	7	90,025,352 (GRCm39)	missense	probably benign	0.00
R8127:Sytl2	UTSW	7	90,024,798 (GRCm39)	missense	possibly damaging	0.93
R8171:Sytl2	UTSW	7	90,058,678 (GRCm39)	missense	probably damaging	1.00
R8225:Sytl2	UTSW	7	90,024,725 (GRCm39)	missense	probably benign	0.36
R8297:Sytl2	UTSW	7	90,034,283 (GRCm39)	missense	probably benign
R8843:Sytl2	UTSW	7	90,025,334 (GRCm39)	missense	probably benign	0.03
R8929:Sytl2	UTSW	7	90,024,810 (GRCm39)	missense	probably benign	0.20
R9027:Sytl2	UTSW	7	90,028,748 (GRCm39)	missense	probably benign	0.00
R9222:Sytl2	UTSW	7	90,050,633 (GRCm39)	missense	possibly damaging	0.81
R9246:Sytl2	UTSW	7	90,007,384 (GRCm39)	missense	probably benign	0.31
R9268:Sytl2	UTSW	7	90,034,359 (GRCm39)	missense	probably benign	0.00
R9399:Sytl2	UTSW	7	90,041,658 (GRCm39)	missense	probably benign	0.23
R9480:Sytl2	UTSW	7	90,020,718 (GRCm39)	missense	possibly damaging	0.92
R9573:Sytl2	UTSW	7	90,057,599 (GRCm39)	missense	probably damaging	1.00
R9583:Sytl2	UTSW	7	90,024,800 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- AATTAGCCCCTAGCATCCATTGCC -3'
(R):5'- AAAGTCATGTCCGAGATAAGCAGGTTC -3'

Sequencing Primer
(F):5'- CTTTGGGAAATGTCACAGACC -3'
(R):5'- AAGGCTACTTTCCAGTGAGC -3'

Posted On

2013-07-11