Incidental Mutation 'R4870:Sytl2'
ID 376505
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 042480-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.384) question?
Stock # R4870 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 89951460-90059927 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 90038106 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 522 (N522I)
Ref Sequence ENSEMBL: ENSMUSP00000139450 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000107210] [ENSMUST00000107211] [ENSMUST00000190731] [ENSMUST00000190837] [ENSMUST00000208720]
AlphaFold Q99N50
Predicted Effect noncoding transcript
Transcript: ENSMUST00000098310
SMART Domains Protein: ENSMUSP00000095912
Gene: ENSMUSG00000030616

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000107210
AA Change: N549I

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000102828
Gene: ENSMUSG00000030616
AA Change: N549I

DomainStartEndE-ValueType
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 benign
Transcript: ENSMUST00000107211
SMART Domains Protein: ENSMUSP00000102829
Gene: ENSMUSG00000030616

DomainStartEndE-ValueType
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: ENSMUST00000190365
Predicted Effect probably damaging
Transcript: ENSMUST00000190731
AA Change: N549I

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000139865
Gene: ENSMUSG00000030616
AA Change: N549I

DomainStartEndE-ValueType
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: N522I

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000139450
Gene: ENSMUSG00000030616
AA Change: N522I

DomainStartEndE-ValueType
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: ENSMUST00000207064
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207928
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208486
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208809
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207431
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207629
Predicted Effect noncoding transcript
Transcript: ENSMUST00000209188
Predicted Effect probably benign
Transcript: ENSMUST00000208720
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207872
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208580
Meta Mutation Damage Score 0.1380 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.1%
Validation Efficiency 100% (77/77)
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb11 A T 2: 69,069,540 (GRCm39) I1285N probably damaging Het
Abcc8 G A 7: 45,756,683 (GRCm39) R721* probably null Het
Alox8 T C 11: 69,077,394 (GRCm39) Y423C probably damaging Het
Ankle2 T A 5: 110,399,344 (GRCm39) probably null Het
Cdc14a A G 3: 116,217,109 (GRCm39) I9T probably benign Het
Ceacam18 T C 7: 43,291,328 (GRCm39) C257R probably damaging Het
Cilp T C 9: 65,186,980 (GRCm39) V1025A probably damaging Het
Clcn7 G T 17: 25,372,539 (GRCm39) probably benign Het
Csnk1d A T 11: 120,874,014 (GRCm39) probably benign Het
Cyp11b2 A G 15: 74,724,995 (GRCm39) S285P probably benign Het
Dip2b T A 15: 100,093,665 (GRCm39) probably null Het
Dmrt1 T A 19: 25,483,219 (GRCm39) M1K probably null Het
Dnajc14 T C 10: 128,653,219 (GRCm39) V684A probably benign Het
Dnmt3b A G 2: 153,512,284 (GRCm39) Q335R probably benign Het
Exoc3l2 T A 7: 19,229,117 (GRCm39) C772S unknown Het
F2rl1 A T 13: 95,650,492 (GRCm39) F130Y probably damaging Het
Galk2 C G 2: 125,771,557 (GRCm39) S194* probably null Het
Garre1 C A 7: 33,984,312 (GRCm39) V104L possibly damaging Het
Gpbp1l1 A G 4: 116,430,714 (GRCm39) T62A probably benign Het
H2-Q10 A T 17: 35,781,357 (GRCm39) D53V probably damaging Het
H2-T22 T C 17: 36,349,924 (GRCm39) K356R probably benign Het
Insrr G A 3: 87,718,911 (GRCm39) V956M probably damaging Het
Ints7 A G 1: 191,328,443 (GRCm39) T239A probably damaging Het
Isl1 A G 13: 116,444,806 (GRCm39) probably benign Het
Kcng2 A G 18: 80,366,083 (GRCm39) C90R probably benign Het
Kif3c C T 12: 3,451,735 (GRCm39) P171S probably damaging Het
Knl1 A G 2: 118,911,994 (GRCm39) T1704A probably benign Het
Lats1 A G 10: 7,581,549 (GRCm39) Y778C probably damaging Het
Limd2 T C 11: 106,050,215 (GRCm39) M1V probably null Het
Mcm10 A T 2: 5,008,970 (GRCm39) I333N probably damaging Het
Mipep T A 14: 61,040,329 (GRCm39) L283* probably null Het
Mixl1 A G 1: 180,522,237 (GRCm39) S215P probably benign Het
Mmp21 A G 7: 133,280,406 (GRCm39) L188P probably damaging Het
Mob1a T C 6: 83,317,221 (GRCm39) S213P probably benign Het
Mplkipl1 C T 19: 61,164,364 (GRCm39) G24R unknown Het
Ndufaf6 T C 4: 11,060,917 (GRCm39) T220A probably benign Het
Nr4a3 A T 4: 48,051,651 (GRCm39) Y135F possibly damaging Het
Ntn1 CCTTCTTCT CCTTCT 11: 68,103,852 (GRCm39) probably benign Het
Obscn A T 11: 59,027,032 (GRCm39) L57Q probably damaging Het
Or52e19b T A 7: 103,032,840 (GRCm39) D123V probably damaging Het
Or5d35 T C 2: 87,855,804 (GRCm39) L246P probably damaging Het
Pirb T A 7: 3,715,661 (GRCm39) M839L probably benign Het
Plcl2 A G 17: 50,914,254 (GRCm39) E421G possibly damaging Het
Ppp1r12b T C 1: 134,876,771 (GRCm39) N99S probably benign Het
Ptpro A G 6: 137,354,130 (GRCm39) K169E probably damaging Het
Rita1 T A 5: 120,749,448 (GRCm39) K88N probably damaging Het
Rptn A T 3: 93,303,776 (GRCm39) K370* probably null Het
Simc1 A G 13: 54,687,576 (GRCm39) D115G probably null Het
Stab1 T A 14: 30,864,000 (GRCm39) N136I probably benign Het
Syt4 T A 18: 31,580,409 (GRCm39) probably benign Het
Tax1bp1 A G 6: 52,706,478 (GRCm39) probably benign Het
Tenm2 A T 11: 35,969,396 (GRCm39) D847E probably damaging Het
Th G T 7: 142,447,834 (GRCm39) D321E probably benign Het
Tmem44 A T 16: 30,359,591 (GRCm39) L46Q probably damaging Het
Trp53bp1 A G 2: 121,087,122 (GRCm39) L178P probably damaging Het
Trp63 A G 16: 25,684,968 (GRCm39) *285W probably null Het
Tsen34 T C 7: 3,697,380 (GRCm39) probably benign Het
Tssk4 C T 14: 55,889,272 (GRCm39) T256I probably benign Het
Ttc17 A T 2: 94,196,954 (GRCm39) N464K probably damaging Het
Ttll2 C T 17: 7,618,998 (GRCm39) V310I probably benign Het
Ubn1 A G 16: 4,895,177 (GRCm39) E741G probably damaging Het
Urad T A 5: 147,252,264 (GRCm39) I63F probably damaging Het
Vcan T C 13: 89,852,858 (GRCm39) T701A probably benign Het
Vmn2r58 A G 7: 41,486,639 (GRCm39) V752A possibly damaging Het
Vmn2r69 C A 7: 85,060,793 (GRCm39) V264L possibly damaging Het
Zfp292 A G 4: 34,808,917 (GRCm39) S1376P probably damaging Het
Zfp955a G A 17: 33,460,699 (GRCm39) R478* probably null Het
Znfx1 A C 2: 166,897,189 (GRCm39) F578L probably benign Het
Other mutations in Sytl2
AlleleSourceChrCoordTypePredicted EffectPPH 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
R0601:Sytl2 UTSW 7 90,044,374 (GRCm39) missense probably damaging 1.00
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
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'- CAAGCTGAAAACCTGTCAGAG -3'
(R):5'- CTTCAGATACACAAGTCTCCTTTAGTG -3'

Sequencing Primer
(F):5'- CAGAGGAACTCTGCAACTT -3'
(R):5'- TGCCAGCTTTGGAGATAT -3'
Posted On 2016-03-17