Incidental Mutation 'R9480:Sytl2'
ID 716186
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
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.384) question?
Stock # R9480 (G1)
Quality Score 225.009
Status Not validated
Chromosome 7
Chromosomal Location 89951460-90059927 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 90020718 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Methionine at position 147 (T147M)
Ref Sequence ENSEMBL: ENSMUSP00000139865 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000107210] [ENSMUST00000107211] [ENSMUST00000190731] [ENSMUST00000190837] [ENSMUST00000207578] [ENSMUST00000208720]
AlphaFold Q99N50
Predicted Effect possibly damaging
Transcript: ENSMUST00000107210
AA Change: T147M

PolyPhen 2 Score 0.950 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000102828
Gene: ENSMUSG00000030616
AA Change: T147M

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 damaging
Transcript: ENSMUST00000107211
AA Change: T147M

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000102829
Gene: ENSMUSG00000030616
AA Change: T147M

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 possibly damaging
Transcript: ENSMUST00000190731
AA Change: T147M

PolyPhen 2 Score 0.916 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000139865
Gene: ENSMUSG00000030616
AA Change: T147M

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: T120M

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000139450
Gene: ENSMUSG00000030616
AA Change: T120M

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 possibly damaging
Transcript: ENSMUST00000207578
AA Change: T147M

PolyPhen 2 Score 0.916 (Sensitivity: 0.81; Specificity: 0.94)
Predicted Effect probably damaging
Transcript: ENSMUST00000208720
AA Change: T147M

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 99.0%
Validation Efficiency
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc1 T A 16: 14,211,889 (GRCm39) W142R probably damaging Het
Abcc6 A G 7: 45,629,197 (GRCm39) S1350P probably damaging Het
Abraxas2 G T 7: 132,473,323 (GRCm39) V84L probably benign Het
Adam12 T A 7: 133,736,470 (GRCm39) I81F probably damaging Het
Adam22 A G 5: 8,193,077 (GRCm39) V376A probably benign Het
Anapc11 T A 11: 120,496,176 (GRCm39) I60N probably damaging Het
Apcdd1 C T 18: 63,055,731 (GRCm39) probably benign Het
Atrnl1 T A 19: 57,690,420 (GRCm39) V876E possibly damaging Het
Bcar3 C T 3: 122,277,618 (GRCm39) R21* probably null Het
Calb1 T A 4: 15,885,608 (GRCm39) S60T probably benign Het
Ceacam9 A G 7: 16,457,783 (GRCm39) T99A probably damaging Het
Cemip2 C A 19: 21,775,622 (GRCm39) H288Q possibly damaging Het
Chst13 G A 6: 90,286,506 (GRCm39) P152L probably damaging Het
Cnot1 T C 8: 96,497,338 (GRCm39) D213G possibly damaging Het
Col23a1 T A 11: 51,207,774 (GRCm39) C105S unknown Het
Cxcl2 T C 5: 91,052,029 (GRCm39) V45A possibly damaging Het
Ddx21 T C 10: 62,434,652 (GRCm39) T36A probably benign Het
Dlgap4 G T 2: 156,546,514 (GRCm39) R394L possibly damaging Het
Dus2 C T 8: 106,757,052 (GRCm39) Q81* probably null Het
Fat3 T C 9: 15,942,703 (GRCm39) D1223G probably damaging Het
Fgf3 G T 7: 144,396,619 (GRCm39) R211L possibly damaging Het
Galnt17 T A 5: 130,935,576 (GRCm39) E369V probably damaging Het
Gatad2a T C 8: 70,388,459 (GRCm39) D76G probably damaging Het
Gin1 A G 1: 97,705,198 (GRCm39) E96G probably damaging Het
Gpr55 A C 1: 85,868,977 (GRCm39) Y201* probably null Het
Hgsnat T C 8: 26,442,029 (GRCm39) N499D possibly damaging Het
Hipk2 G T 6: 38,680,377 (GRCm39) P988T probably benign Het
Hivep1 A T 13: 42,337,058 (GRCm39) Q2379L probably damaging Het
Kat14 T A 2: 144,215,745 (GRCm39) C77S probably damaging Het
Klhl25 T C 7: 75,516,120 (GRCm39) V342A probably damaging Het
Krt35 T C 11: 99,986,609 (GRCm39) Q135R probably benign Het
Lhfpl2 T A 13: 94,310,733 (GRCm39) M1K probably null Het
Lipk T A 19: 33,999,101 (GRCm39) L132Q probably damaging Het
Lrrc39 T A 3: 116,359,475 (GRCm39) C7S probably benign Het
Ltb4r2 T A 14: 56,000,089 (GRCm39) W237R probably damaging Het
Mesp2 A G 7: 79,461,034 (GRCm39) I120V probably damaging Het
Mfsd6 A G 1: 52,699,835 (GRCm39) V771A unknown Het
Mtfmt A T 9: 65,351,181 (GRCm39) T243S possibly damaging Het
Nlrp12 A T 7: 3,288,993 (GRCm39) C506* probably null Het
Ntng2 T A 2: 29,137,997 (GRCm39) Y19F probably damaging Het
Nxt2 C T X: 141,020,747 (GRCm39) A118V possibly damaging Het
Orc4 T C 2: 48,795,563 (GRCm39) T388A probably benign Het
P4hb A T 11: 120,463,551 (GRCm39) V28D probably damaging Het
Phkb T G 8: 86,684,216 (GRCm39) S424R probably benign Het
Poldip2 T C 11: 78,411,988 (GRCm39) L308S probably damaging Het
Prkd1 T A 12: 50,435,283 (GRCm39) E481D probably benign Het
Serping1 C T 2: 84,600,487 (GRCm39) S285N probably benign Het
Sh2d2a A C 3: 87,759,638 (GRCm39) I350L probably benign Het
Siglecf G T 7: 43,001,666 (GRCm39) V159L possibly damaging Het
Sspo A G 6: 48,470,820 (GRCm39) N36S probably damaging Het
Tmc7 A G 7: 118,141,226 (GRCm39) F635S probably benign Het
Tmco1 C T 1: 167,157,757 (GRCm39) L175F Het
Ttc39d A G 17: 80,524,139 (GRCm39) H266R probably benign Het
Usp33 T G 3: 152,079,086 (GRCm39) I446R possibly damaging Het
Usp48 G A 4: 137,340,996 (GRCm39) G332E probably benign Het
Zbtb49 T A 5: 38,358,409 (GRCm39) T615S possibly damaging Het
Zbtb8a G T 4: 129,253,875 (GRCm39) H206Q probably benign Het
Zfp180 A G 7: 23,804,628 (GRCm39) N349S probably benign Het
Zfp345 A T 2: 150,315,212 (GRCm39) C108* probably null Het
Zfp420 T A 7: 29,575,497 (GRCm39) H572Q probably benign Het
Zfp423 A G 8: 88,631,115 (GRCm39) probably null Het
Zfp820 T A 17: 22,037,994 (GRCm39) T445S possibly damaging Het
Zim1 T C 7: 6,681,050 (GRCm39) I204M probably benign Het
Zpld2 G A 4: 133,929,312 (GRCm39) P331L 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
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
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'- TCCCTAATCATGGCTGGAGC -3'
(R):5'- AGCTGGACCTTTAGCAACAC -3'

Sequencing Primer
(F):5'- GGAGCCCAGTTTCTTCTCC -3'
(R):5'- ATTATCAACTTTATCCACCCCCGGAG -3'
Posted On 2022-07-18