Mutagenetix > Incidental Mutation

Incidental Mutation 'R4651:Sytl2'

351291

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

041911-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.302) question?

Stock #

R4651 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

89951460-90059927 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 90024633 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Glutamine at position 207 (P207Q)

Ref Sequence

ENSEMBL: ENSMUSP00000146353 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000107210] [ENSMUST00000107211] [ENSMUST00000190731] [ENSMUST00000190837] [ENSMUST00000207578] [ENSMUST00000208720]

AlphaFold

Q99N50

Predicted Effect

probably benign
Transcript: ENSMUST00000107210
AA Change: P207Q

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000102828
Gene: ENSMUSG00000030616
AA Change: P207Q

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 benign
Transcript: ENSMUST00000107211
AA Change: P207Q

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000102829
Gene: ENSMUSG00000030616
AA Change: P207Q

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

probably benign
Transcript: ENSMUST00000190731
AA Change: P207Q

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000139865
Gene: ENSMUSG00000030616
AA Change: P207Q

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 benign
Transcript: ENSMUST00000190837
AA Change: P180Q

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000139450
Gene: ENSMUSG00000030616
AA Change: P180Q

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: ENSMUST00000207455

Predicted Effect

probably damaging
Transcript: ENSMUST00000207578
AA Change: P207Q

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

Predicted Effect

probably benign
Transcript: ENSMUST00000208720
AA Change: P207Q

PolyPhen 2 Score 0.048 (Sensitivity: 0.94; Specificity: 0.83)

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

97% (98/101)

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	G	T	12: 71,211,320 (GRCm39)	E685*	probably null	Het
2700049A03Rik	A	T	12: 71,211,321 (GRCm39)	E685V	possibly damaging	Het
4933409G03Rik	G	A	2: 68,436,559 (GRCm39)	E168K	unknown	Het
Ahnak2	T	G	12: 112,741,271 (GRCm39)	S128R	possibly damaging	Het
Ankrd26	T	C	6: 118,492,787 (GRCm39)	D1319G	probably benign	Het
Ankrd35	T	C	3: 96,591,343 (GRCm39)	V543A	probably benign	Het
Ano10	A	T	9: 122,090,181 (GRCm39)	Y377*	probably null	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
Atp10b	G	A	11: 43,085,472 (GRCm39)	G284S	probably damaging	Het
Atp5f1c	A	G	2: 10,068,287 (GRCm39)	F180S	probably damaging	Het
Btnl4	A	G	17: 34,691,602 (GRCm39)	S296P	probably benign	Het
Cast	A	G	13: 74,894,133 (GRCm39)	S171P	probably benign	Het
Catsperb	G	A	12: 101,507,771 (GRCm39)	A513T	probably benign	Het
Ccnf	C	A	17: 24,450,760 (GRCm39)	R406L	probably damaging	Het
Ceacam12	A	G	7: 17,801,359 (GRCm39)	T113A	probably damaging	Het
Cipc	T	C	12: 87,008,864 (GRCm39)	V241A	probably benign	Het
Col12a1	A	T	9: 79,520,228 (GRCm39)	D2815E	probably damaging	Het
Cpox	G	T	16: 58,491,050 (GRCm39)	R87L	possibly damaging	Het
Cttnbp2	A	G	6: 18,434,037 (GRCm39)	I607T	possibly damaging	Het
Cux1	A	T	5: 136,596,083 (GRCm39)	N4K	probably damaging	Het
Cyp3a25	T	C	5: 145,931,701 (GRCm39)	T136A	probably benign	Het
Dhx58	T	A	11: 100,592,185 (GRCm39)	N288Y	probably damaging	Het
Dnah10	T	C	5: 124,806,207 (GRCm39)	Y127H	probably benign	Het
Dnd1	G	A	18: 36,898,114 (GRCm39)		probably benign	Het
Ehmt2	C	A	17: 35,132,790 (GRCm39)	N1171K	probably damaging	Het
Fanci	T	A	7: 79,085,004 (GRCm39)	M838K	possibly damaging	Het
Flot1	T	C	17: 36,143,436 (GRCm39)		probably benign	Het
Gad2	A	T	2: 22,558,374 (GRCm39)	D364V	probably damaging	Het
Gm10375	C	A	14: 43,844,326 (GRCm39)		probably null	Het
Gm9996	T	A	10: 29,019,754 (GRCm39)		probably benign	Het
Gnat3	T	A	5: 18,220,568 (GRCm39)	L247H	probably damaging	Het
Ip6k3	C	T	17: 27,364,265 (GRCm39)	C261Y	probably damaging	Het
Irgc	C	A	7: 24,132,238 (GRCm39)	R193L	probably damaging	Het
Kalrn	G	T	16: 33,996,761 (GRCm39)	P1477Q	probably damaging	Het
Kyat1	G	T	2: 30,084,076 (GRCm39)	H15N	probably benign	Het
Lamc1	T	G	1: 153,104,523 (GRCm39)	S59R	probably damaging	Het
Llgl1	A	G	11: 60,599,477 (GRCm39)	D486G	possibly damaging	Het
Lrrc9	T	C	12: 72,524,160 (GRCm39)	W790R	probably damaging	Het
Lsm2	T	A	17: 35,204,571 (GRCm39)		probably benign	Het
Med8	A	T	4: 118,268,089 (GRCm39)	E5V	probably damaging	Het
Mefv	A	G	16: 3,535,682 (GRCm39)	L82P	probably damaging	Het
Mettl25b	T	C	3: 87,834,979 (GRCm39)	H107R	probably benign	Het
Mettl3	T	A	14: 52,532,549 (GRCm39)	I545F	probably damaging	Het
Naa20	CTCTAGA	C	2: 145,753,752 (GRCm39)		probably benign	Het
Ncapg2	T	A	12: 116,389,407 (GRCm39)	N342K	probably damaging	Het
Ndufaf6	T	A	4: 11,062,070 (GRCm39)	Y187F	probably damaging	Het
Nomo1	T	A	7: 45,717,866 (GRCm39)	I799N	probably damaging	Het
Obscn	G	A	11: 58,929,703 (GRCm39)	R5824C	probably damaging	Het
Or4f6	G	T	2: 111,838,595 (GRCm39)	S312Y	probably damaging	Het
Or6c214	T	C	10: 129,591,287 (GRCm39)	I11V	probably benign	Het
Or6n2	A	G	1: 173,897,394 (GRCm39)	I177V	possibly damaging	Het
Or7g30	T	A	9: 19,352,591 (GRCm39)	C127*	probably null	Het
Pgm3	T	A	9: 86,440,523 (GRCm39)	R389S	probably benign	Het
Pkd2l2	A	T	18: 34,542,889 (GRCm39)	R20*	probably null	Het
Pkhd1	T	A	1: 20,451,747 (GRCm39)	I2183F	probably damaging	Het
Ppp4r3a	T	A	12: 101,049,170 (GRCm39)		probably benign	Het
Prpf38b	G	A	3: 108,811,408 (GRCm39)		probably benign	Het
Prpf4b	A	T	13: 35,083,954 (GRCm39)	M908L	probably benign	Het
Prps2	T	C	X: 166,135,288 (GRCm39)	D183G	probably damaging	Het
Prrc2c	A	T	1: 162,550,843 (GRCm39)	H40Q	probably damaging	Het
Ptprk	T	C	10: 28,139,686 (GRCm39)	I137T	probably damaging	Het
Sdr42e1	T	C	8: 118,390,360 (GRCm39)	T94A	probably benign	Het
Setd2	A	G	9: 110,423,200 (GRCm39)	D2085G	possibly damaging	Het
Sgce	T	C	6: 4,689,560 (GRCm39)		probably benign	Het
Shisa3	A	G	5: 67,765,992 (GRCm39)	D81G	probably damaging	Het
Sipa1l1	T	A	12: 82,469,245 (GRCm39)	L1248*	probably null	Het
Skint7	T	G	4: 111,839,309 (GRCm39)	M201R	probably damaging	Het
Slc5a3	T	A	16: 91,874,090 (GRCm39)	V49E	probably benign	Het
Slc9c1	A	T	16: 45,367,756 (GRCm39)	*163L	probably null	Het
Smyd3	A	G	1: 178,871,306 (GRCm39)	Y358H	probably benign	Het
Srp68	A	T	11: 116,164,840 (GRCm39)	S31R	probably benign	Het
Stag1	T	A	9: 100,678,769 (GRCm39)	M230K	probably damaging	Het
Strc	A	T	2: 121,204,829 (GRCm39)	D985E	possibly damaging	Het
Syne2	A	G	12: 76,036,013 (GRCm39)	T3767A	probably damaging	Het
Tbc1d2b	A	G	9: 90,089,940 (GRCm39)	F863S	probably damaging	Het
Tek	T	C	4: 94,669,121 (GRCm39)	S41P	probably damaging	Het
Top1	T	C	2: 160,554,637 (GRCm39)	Y463H	probably damaging	Het
Trim24	T	G	6: 37,934,774 (GRCm39)		probably null	Het
Trim38	A	T	13: 23,966,952 (GRCm39)	D133V	probably damaging	Het
Ttn	A	G	2: 76,576,979 (GRCm39)	V24638A	possibly damaging	Het
Ttn	A	G	2: 76,701,213 (GRCm39)		probably benign	Het
Tyro3	G	C	2: 119,647,349 (GRCm39)	G826A	probably benign	Het
Ube2b	A	G	11: 51,886,199 (GRCm39)		probably null	Het
Ubxn4	T	A	1: 128,202,587 (GRCm39)	W410R	probably benign	Het
Unc45a	T	C	7: 79,982,777 (GRCm39)	K383E	possibly damaging	Het
Usp7	A	C	16: 8,516,278 (GRCm39)		probably benign	Het
Vmn1r193	C	T	13: 22,403,695 (GRCm39)	G99D	probably damaging	Het
Vrk2	T	C	11: 26,439,803 (GRCm39)	D256G	probably damaging	Het
Wdr81	A	G	11: 75,342,066 (GRCm39)	V1067A	probably damaging	Het
Wiz	C	T	17: 32,576,655 (GRCm39)	R624Q	probably damaging	Het
Zcwpw2	A	G	9: 117,843,119 (GRCm39)		noncoding transcript	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
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
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'- AAGTGCTTTTCCCATTAGGTCTGC -3'
(R):5'- GCGCTTTAGGATCCCTCTTG -3'

Sequencing Primer
(F):5'- TCCCATTAGGTCTGCATTTATGC -3'
(R):5'- GAGCCCCTCTCGCATTCAG -3'

Posted On

2015-10-08