Incidental Mutation 'R0541:Stx5a'
ID 49947
Institutional Source Beutler Lab
Gene Symbol Stx5a
Ensembl Gene ENSMUSG00000010110
Gene Name syntaxin 5A
Synonyms syntaxin 5, 0610031F24Rik, D19Ertd627e
MMRRC Submission 038733-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0541 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 8718788-8733006 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 8727301 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Threonine at position 177 (M177T)
Ref Sequence ENSEMBL: ENSMUSP00000134794 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000010254] [ENSMUST00000073430] [ENSMUST00000175872] [ENSMUST00000175901] [ENSMUST00000176968] [ENSMUST00000177373] [ENSMUST00000176381] [ENSMUST00000176570] [ENSMUST00000177322] [ENSMUST00000176013]
AlphaFold Q8K1E0
Predicted Effect probably damaging
Transcript: ENSMUST00000010254
AA Change: M273T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000010254
Gene: ENSMUSG00000010110
AA Change: M273T

DomainStartEndE-ValueType
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: M273T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000073136
Gene: ENSMUSG00000010110
AA Change: M273T

DomainStartEndE-ValueType
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 probably benign
Transcript: ENSMUST00000175872
SMART Domains Protein: ENSMUSP00000135416
Gene: ENSMUSG00000010110

DomainStartEndE-ValueType
low complexity region 26 44 N/A INTRINSIC
Pfam:Syntaxin 90 194 2.7e-16 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000175901
SMART Domains Protein: ENSMUSP00000134951
Gene: ENSMUSG00000010110

DomainStartEndE-ValueType
low complexity region 26 44 N/A INTRINSIC
Pfam:Syntaxin 90 194 4e-16 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176009
Predicted Effect possibly damaging
Transcript: ENSMUST00000176968
AA Change: M27T

PolyPhen 2 Score 0.919 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000135468
Gene: ENSMUSG00000010110
AA Change: M27T

DomainStartEndE-ValueType
t_SNARE 12 79 4.33e-15 SMART
transmembrane domain 88 107 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000177373
AA Change: M177T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000134794
Gene: ENSMUSG00000010110
AA Change: M177T

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000176381
AA Change: M273T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000134854
Gene: ENSMUSG00000010110
AA Change: M273T

DomainStartEndE-ValueType
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: ENSMUST00000176570
AA Change: M27T

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000134892
Gene: ENSMUSG00000010110
AA Change: M27T

DomainStartEndE-ValueType
Pfam:SNARE 22 57 2.9e-12 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176404
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176844
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176182
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176260
Predicted Effect probably benign
Transcript: ENSMUST00000177322
SMART Domains Protein: ENSMUSP00000135624
Gene: ENSMUSG00000010110

DomainStartEndE-ValueType
low complexity region 26 44 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000176013
SMART Domains Protein: ENSMUSP00000135465
Gene: ENSMUSG00000010110

DomainStartEndE-ValueType
low complexity region 26 44 N/A INTRINSIC
Pfam:Syntaxin 90 143 3e-8 PFAM
Meta Mutation Damage Score 0.9159 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.9%
Validation Efficiency 96% (64/67)
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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933402N03Rik T C 7: 130,740,872 (GRCm39) M115V probably benign Het
4933415A04Rik TTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT TTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 11: 43,478,227 (GRCm39) probably null Het
Abca7 C T 10: 79,843,185 (GRCm39) A1220V probably benign Het
Adamts19 G A 18: 59,060,372 (GRCm39) probably null Het
Agbl1 G A 7: 76,058,993 (GRCm39) V194M probably benign Het
Arhgap20 G T 9: 51,760,963 (GRCm39) S902I probably damaging Het
Atp11b T G 3: 35,861,093 (GRCm39) D193E probably damaging Het
B3gntl1 A T 11: 121,535,430 (GRCm39) probably benign Het
C2cd2 T C 16: 97,723,496 (GRCm39) E7G possibly damaging Het
Camta2 A G 11: 70,572,447 (GRCm39) L259P probably benign Het
Ccni T C 5: 93,335,563 (GRCm39) N192D probably benign Het
Cgnl1 A G 9: 71,558,535 (GRCm39) I946T possibly damaging Het
Chil3 T C 3: 106,068,548 (GRCm39) probably null Het
Cntn5 A G 9: 9,673,407 (GRCm39) probably benign Het
Cpn2 C T 16: 30,078,169 (GRCm39) G511S possibly damaging Het
Dagla C A 19: 10,232,170 (GRCm39) probably null Het
Dcc T C 18: 71,392,086 (GRCm39) N1440S probably damaging Het
Drosha T A 15: 12,907,474 (GRCm39) N1069K probably benign Het
Edc4 A G 8: 106,616,060 (GRCm39) T812A probably benign Het
Eml4 A G 17: 83,747,471 (GRCm39) I238V probably benign Het
Ep400 T C 5: 110,852,882 (GRCm39) T1288A unknown Het
Fastkd1 A C 2: 69,532,750 (GRCm39) L539R probably damaging Het
Fbln7 G A 2: 128,719,454 (GRCm39) probably benign Het
Fbxo39 A G 11: 72,209,297 (GRCm39) I386V probably benign Het
Gm17430 T C 18: 9,726,267 (GRCm39) K135R probably damaging Het
Gm3646 T A 1: 39,843,483 (GRCm39) T8S unknown Het
Gtsf1 A T 15: 103,329,619 (GRCm39) V100E possibly damaging Het
Helz2 A G 2: 180,876,618 (GRCm39) F1292S possibly damaging Het
Igf2bp3 G A 6: 49,084,401 (GRCm39) probably benign Het
Ip6k2 T G 9: 108,681,826 (GRCm39) D252E probably damaging Het
Iqck T A 7: 118,514,817 (GRCm39) L232Q probably damaging Het
Kif18b A G 11: 102,806,001 (GRCm39) V186A probably damaging Het
Klhl6 T A 16: 19,768,197 (GRCm39) probably null Het
Lao1 C T 4: 118,820,999 (GRCm39) T75I probably benign Het
Lyst T C 13: 13,855,878 (GRCm39) F2400L probably benign Het
Map3k9 A T 12: 81,780,997 (GRCm39) S388T possibly damaging Het
Mmp11 G T 10: 75,762,767 (GRCm39) H229N probably damaging Het
Myh7 T G 14: 55,212,158 (GRCm39) I1529L probably benign Het
Nckap5 G T 1: 126,623,459 (GRCm39) D11E possibly damaging Het
Ncoa1 A T 12: 4,373,033 (GRCm39) F123I probably damaging Het
Nelfb A T 2: 25,093,992 (GRCm39) D385E probably benign Het
Obscn C T 11: 58,972,810 (GRCm39) V2288M probably damaging Het
Or2f1b A G 6: 42,739,154 (GRCm39) H56R probably damaging Het
Or4d6 C T 19: 12,086,884 (GRCm39) V9M possibly damaging Het
Or52x1 A T 7: 104,853,367 (GRCm39) M61K probably damaging Het
Or5b12b A G 19: 12,861,458 (GRCm39) Y71C probably damaging Het
Otog T A 7: 45,918,673 (GRCm39) probably benign Het
Oxa1l A G 14: 54,605,646 (GRCm39) E375G possibly damaging Het
Pan2 T A 10: 128,144,091 (GRCm39) I129K possibly damaging Het
Parp1 A G 1: 180,426,616 (GRCm39) I919M probably benign Het
Pnpla7 T C 2: 24,885,305 (GRCm39) Y174H probably damaging Het
Polr3b T C 10: 84,473,928 (GRCm39) F169S probably damaging Het
Rab10 T C 12: 3,314,743 (GRCm39) D45G probably damaging Het
Reln A G 5: 22,185,107 (GRCm39) S1537P possibly damaging Het
Sema6d T A 2: 124,507,197 (GRCm39) S1045T probably benign Het
Setd2 T C 9: 110,402,741 (GRCm39) V1794A probably damaging Het
Spidr T A 16: 15,733,229 (GRCm39) I589F probably damaging Het
Stmn4 A C 14: 66,595,388 (GRCm39) I165L probably benign Het
Tll1 T C 8: 64,491,486 (GRCm39) probably null Het
Tmem192 T C 8: 65,416,912 (GRCm39) Y168H probably damaging Het
Ttc21a C T 9: 119,785,892 (GRCm39) probably benign Het
Ush2a A G 1: 188,446,663 (GRCm39) probably benign Het
Vezf1 A G 11: 87,972,403 (GRCm39) M255V possibly damaging Het
Vmn2r25 A G 6: 123,816,786 (GRCm39) F265S probably damaging Het
Vps13a A G 19: 16,681,941 (GRCm39) S1021P probably benign Het
Wfdc16 T C 2: 164,477,773 (GRCm39) E92G possibly damaging Het
Zkscan2 T C 7: 123,079,423 (GRCm39) T845A possibly damaging Het
Other mutations in Stx5a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03152:Stx5a APN 19 8,727,138 (GRCm39) critical splice donor site probably null
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
R5594:Stx5a UTSW 19 8,725,829 (GRCm39) missense probably damaging 1.00
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'- CATGATGGACCCTAGAACAAGCCAG -3'
(R):5'- GAAATGCCTTTGCCGGATGAGC -3'

Sequencing Primer
(F):5'- CAGCAGCTTCAGCTCATTG -3'
(R):5'- gctctgcctgtttgtgtctc -3'
Posted On 2013-06-12