Mutagenetix > Incidental Mutation

Incidental Mutation 'R5594:Stx5a'

437743

Institutional Source

Beutler Lab

Gene Symbol

Stx5a

Ensembl Gene

ENSMUSG00000010110

Gene Name

syntaxin 5A

Synonyms

syntaxin 5, 0610031F24Rik, D19Ertd627e

MMRRC Submission

043146-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5594 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

8718788-8733006 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 8725829 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 143 (I143T)

Ref Sequence

ENSEMBL: ENSMUSP00000134854 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000010254] [ENSMUST00000073430] [ENSMUST00000175872] [ENSMUST00000175901] [ENSMUST00000176013] [ENSMUST00000176381] [ENSMUST00000177373] [ENSMUST00000176968] [ENSMUST00000177322] [ENSMUST00000176570]

AlphaFold

Q8K1E0

Predicted Effect

probably damaging
Transcript: ENSMUST00000010254
AA Change: I143T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000010254
Gene: ENSMUSG00000010110
AA Change: I143T

Domain	Start	End	E-Value	Type
low complexity region	26	44	N/A	INTRINSIC
Pfam:Syntaxin-5_N	52	74	1.5e-15	PFAM
SCOP:d1fioa_	92	298	7e-36	SMART
Blast:t_SNARE	258	304	9e-22	BLAST
low complexity region	346	376	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000073430
AA Change: I143T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000073136
Gene: ENSMUSG00000010110
AA Change: I143T

Domain	Start	End	E-Value	Type
low complexity region	26	44	N/A	INTRINSIC
Pfam:Syntaxin	90	194	1e-15	PFAM
t_SNARE	258	325	4.33e-15	SMART
transmembrane domain	334	353	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175834

Predicted Effect

possibly damaging
Transcript: ENSMUST00000175872
AA Change: I143T

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000135416
Gene: ENSMUSG00000010110
AA Change: I143T

Domain	Start	End	E-Value	Type
low complexity region	26	44	N/A	INTRINSIC
Pfam:Syntaxin	90	194	2.7e-16	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000175901
AA Change: I143T

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000134951
Gene: ENSMUSG00000010110
AA Change: I143T

Domain	Start	End	E-Value	Type
low complexity region	26	44	N/A	INTRINSIC
Pfam:Syntaxin	90	194	4e-16	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176009

Predicted Effect

probably benign
Transcript: ENSMUST00000176013

SMART Domains

Protein: ENSMUSP00000135465
Gene: ENSMUSG00000010110

Domain	Start	End	E-Value	Type
low complexity region	26	44	N/A	INTRINSIC
Pfam:Syntaxin	90	143	3e-8	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000176381
AA Change: I143T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000134854
Gene: ENSMUSG00000010110
AA Change: I143T

Domain	Start	End	E-Value	Type
low complexity region	26	44	N/A	INTRINSIC
Pfam:Syntaxin	90	194	1e-15	PFAM
t_SNARE	258	325	4.33e-15	SMART
transmembrane domain	334	353	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000177373
AA Change: I47T

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000134794
Gene: ENSMUSG00000010110
AA Change: I47T

Domain	Start	End	E-Value	Type
Pfam:Syntaxin	1	98	5.2e-15	PFAM
t_SNARE	162	229	4.33e-15	SMART
transmembrane domain	238	257	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176182

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176404

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176844

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176093

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176260

Predicted Effect

probably benign
Transcript: ENSMUST00000176968

SMART Domains

Protein: ENSMUSP00000135468
Gene: ENSMUSG00000010110

Domain	Start	End	E-Value	Type
t_SNARE	12	79	4.33e-15	SMART
transmembrane domain	88	107	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000177322

SMART Domains

Protein: ENSMUSP00000135624
Gene: ENSMUSG00000010110

Domain	Start	End	E-Value	Type
low complexity region	26	44	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000176570

SMART Domains

Protein: ENSMUSP00000134892
Gene: ENSMUSG00000010110

Domain	Start	End	E-Value	Type
Pfam:SNARE	22	57	2.9e-12	PFAM

Meta Mutation Damage Score

0.7002

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.7%
20x: 96.4%

Validation Efficiency

100% (80/80)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the syntaxin or t-SNARE (target-SNAP receptor) family. These proteins are found on cell membranes and serve as the targets for v-SNAREs (vesicle-SNAP receptors), permitting specific synaptic vesicle docking and fusion. The encoded protein regulates endoplasmic reticulum to Golgi transport and plays a critical role in autophagy. Autoantibodies targeting the encoded protein may be a diagnostic marker for endometriosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930556J24Rik	C	T	11: 3,888,027 (GRCm39)	V120I	unknown	Het
4931414P19Rik	A	G	14: 54,822,441 (GRCm39)	Y399H	probably damaging	Het
Abca9	G	T	11: 110,035,688 (GRCm39)	P644Q	probably damaging	Het
Acly	T	C	11: 100,412,946 (GRCm39)		probably null	Het
Adamts14	A	T	10: 61,062,880 (GRCm39)		probably null	Het
Ankdd1a	T	C	9: 65,409,523 (GRCm39)	N471S	probably damaging	Het
Ankrd39	C	T	1: 36,581,062 (GRCm39)	G96R	probably damaging	Het
Arhgef28	T	C	13: 98,076,000 (GRCm39)	T1345A	probably benign	Het
Arhgef40	T	A	14: 52,233,614 (GRCm39)	L820H	probably damaging	Het
Atp2b4	A	G	1: 133,658,248 (GRCm39)	V554A	probably damaging	Het
Birc7	G	A	2: 180,575,129 (GRCm39)		probably null	Het
Ccdc80	C	T	16: 44,936,626 (GRCm39)	R684C	probably benign	Het
Cdc25b	C	A	2: 131,033,538 (GRCm39)	P159Q	probably damaging	Het
Cdcp3	T	A	7: 130,841,252 (GRCm39)	D647E	probably benign	Het
Chek2	G	T	5: 111,003,700 (GRCm39)		probably null	Het
Chil6	C	T	3: 106,301,745 (GRCm39)		probably null	Het
Cr2	A	G	1: 194,839,498 (GRCm39)	I643T	probably damaging	Het
Cwf19l2	C	A	9: 3,418,773 (GRCm39)	Q187K	probably benign	Het
Cyth4	A	G	15: 78,491,275 (GRCm39)		probably null	Het
Depdc5	A	G	5: 33,058,834 (GRCm39)	T268A	possibly damaging	Het
Dnah17	G	T	11: 117,934,055 (GRCm39)		probably null	Het
Dnah3	T	C	7: 119,570,844 (GRCm39)	Y2210C	possibly damaging	Het
Elmod3	G	A	6: 72,571,799 (GRCm39)		probably benign	Het
Eogt	T	A	6: 97,092,996 (GRCm39)	T394S	probably benign	Het
Evi5	A	G	5: 107,968,317 (GRCm39)	V182A	possibly damaging	Het
Fbxo30	T	C	10: 11,166,223 (GRCm39)	I315T	probably benign	Het
Fibcd1	T	C	2: 31,728,629 (GRCm39)	N76S	probably damaging	Het
Gcc2	G	T	10: 58,123,064 (GRCm39)	R1190M	probably damaging	Het
Gfm2	T	C	13: 97,301,546 (GRCm39)	S450P	probably damaging	Het
Glg1	G	A	8: 111,914,513 (GRCm39)	R424C	probably damaging	Het
Gm11543	T	A	11: 94,719,380 (GRCm39)		noncoding transcript	Het
Hhip	G	T	8: 80,723,492 (GRCm39)	D387E	probably damaging	Het
Hif1a	T	A	12: 73,984,566 (GRCm39)	Y46*	probably null	Het
Hivep3	G	T	4: 119,980,245 (GRCm39)		probably null	Het
Kif13a	T	A	13: 46,906,338 (GRCm39)	E535V	probably damaging	Het
Lrch3	T	C	16: 32,734,554 (GRCm39)	Y15H	probably damaging	Het
Lyst	T	G	13: 13,917,918 (GRCm39)	I3326S	probably damaging	Het
Lyst	T	A	13: 13,933,982 (GRCm39)	V3560E	probably benign	Het
Megf11	T	C	9: 64,593,755 (GRCm39)	F613L	probably damaging	Het
Misp	G	A	10: 79,662,977 (GRCm39)	V465M	probably damaging	Het
Mplkipl1	C	T	19: 61,164,364 (GRCm39)	G24R	unknown	Het
Ms4a6c	T	A	19: 11,455,537 (GRCm39)	D115E	probably benign	Het
Msh6	A	G	17: 88,293,497 (GRCm39)	T751A	probably benign	Het
Ntrk3	T	A	7: 78,101,647 (GRCm39)	T429S	probably benign	Het
Oplah	A	C	15: 76,180,837 (GRCm39)	*1289G	probably null	Het
Or14j7	T	A	17: 38,234,502 (GRCm39)	M15K	probably benign	Het
Or7e166	T	C	9: 19,624,302 (GRCm39)	Y60H	probably damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Pcdhga6	A	T	18: 37,841,581 (GRCm39)	T434S	probably benign	Het
Pign	A	G	1: 105,574,594 (GRCm39)		probably benign	Het
Poteg	A	T	8: 27,937,996 (GRCm39)	I51F	probably benign	Het
Prrc2c	C	A	1: 162,526,600 (GRCm39)	V204F	unknown	Het
Rhbdd3	T	C	11: 5,055,710 (GRCm39)	S325P	probably damaging	Het
Rit1	T	A	3: 88,636,444 (GRCm39)	L116Q	probably damaging	Het
Rpl22	T	A	4: 152,410,259 (GRCm39)		probably benign	Het
Rttn	A	G	18: 89,108,560 (GRCm39)	E1588G	possibly damaging	Het
Sardh	A	G	2: 27,110,735 (GRCm39)	F577S	probably damaging	Het
Slc12a7	T	A	13: 73,933,258 (GRCm39)	D105E	probably benign	Het
Slc22a23	T	A	13: 34,489,240 (GRCm39)	D215V	probably damaging	Het
Slc4a8	C	A	15: 100,693,768 (GRCm39)	P438T	probably damaging	Het
Sntb1	C	G	15: 55,506,191 (GRCm39)	G461R	probably damaging	Het
Stk19	C	T	17: 35,039,538 (GRCm39)		probably benign	Het
Tep1	T	C	14: 51,067,339 (GRCm39)	H2232R	possibly damaging	Het
Trmt9b	A	G	8: 36,979,452 (GRCm39)	T352A	probably benign	Het
Ttc21b	A	G	2: 66,066,579 (GRCm39)	I358T	probably benign	Het
Tuba8	A	G	6: 121,202,863 (GRCm39)	D392G	possibly damaging	Het
Vmn1r1	G	A	1: 181,984,972 (GRCm39)	P231L	probably damaging	Het
Zfp330	A	G	8: 83,493,941 (GRCm39)	W107R	probably damaging	Het
Zfp715	T	A	7: 42,949,116 (GRCm39)	Q281H	possibly damaging	Het
Zfp9	T	C	6: 118,442,000 (GRCm39)	T221A	probably damaging	Het
Zgpat	T	C	2: 181,007,420 (GRCm39)		probably benign	Het

Other mutations in Stx5a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03152:Stx5a	APN	19	8,727,138 (GRCm39)	critical splice donor site	probably null
R0541:Stx5a	UTSW	19	8,727,301 (GRCm39)	missense	probably damaging	1.00
R0726:Stx5a	UTSW	19	8,732,275 (GRCm39)	missense	probably damaging	1.00
R1566:Stx5a	UTSW	19	8,719,675 (GRCm39)	missense	probably damaging	0.99
R1990:Stx5a	UTSW	19	8,726,254 (GRCm39)	critical splice donor site	probably null
R2852:Stx5a	UTSW	19	8,732,476 (GRCm39)	unclassified	probably benign
R3022:Stx5a	UTSW	19	8,732,518 (GRCm39)	unclassified	probably benign
R4426:Stx5a	UTSW	19	8,727,104 (GRCm39)	missense	probably benign	0.02
R4684:Stx5a	UTSW	19	8,720,725 (GRCm39)	missense	probably damaging	0.96
R5750:Stx5a	UTSW	19	8,732,501 (GRCm39)	unclassified	probably benign
R5929:Stx5a	UTSW	19	8,719,675 (GRCm39)	missense	probably damaging	0.99
R6644:Stx5a	UTSW	19	8,732,612 (GRCm39)	unclassified	probably benign
R6983:Stx5a	UTSW	19	8,732,533 (GRCm39)	unclassified	probably benign
R7242:Stx5a	UTSW	19	8,732,641 (GRCm39)	missense	unknown
R7258:Stx5a	UTSW	19	8,732,271 (GRCm39)	critical splice acceptor site	probably null
R7464:Stx5a	UTSW	19	8,720,868 (GRCm39)	unclassified	probably benign
R7871:Stx5a	UTSW	19	8,732,482 (GRCm39)	missense	unknown
R7880:Stx5a	UTSW	19	8,719,692 (GRCm39)	missense	probably damaging	1.00
R7980:Stx5a	UTSW	19	8,719,802 (GRCm39)	missense	probably damaging	1.00
R8375:Stx5a	UTSW	19	8,732,462 (GRCm39)	missense	unknown
R8739:Stx5a	UTSW	19	8,725,924 (GRCm39)	missense	probably damaging	0.96
X0020:Stx5a	UTSW	19	8,726,254 (GRCm39)	critical splice donor site	probably benign

Predicted Primers

PCR Primer
(F):5'- TTCTCTGCTAGGAATGAACAGAGC -3'
(R):5'- TGGACATAGAAGCCAGCTTTG -3'

Sequencing Primer
(F):5'- CTAGAAAAGTCTAGTGTCACCTTCTG -3'
(R):5'- GCCAGCTTTGACTAAAAGGC -3'

Posted On

2016-10-26