Incidental Mutation 'R1451:Snx13'
ID 161686
Institutional Source Beutler Lab
Gene Symbol Snx13
Ensembl Gene ENSMUSG00000020590
Gene Name sorting nexin 13
Synonyms RGS-PX1
MMRRC Submission 039506-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1451 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 35097191-35197479 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 35128983 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Threonine at position 34 (A34T)
Ref Sequence ENSEMBL: ENSMUSP00000152167 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000048519] [ENSMUST00000163677] [ENSMUST00000221272]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000048519
AA Change: A34T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000038430
Gene: ENSMUSG00000020590
AA Change: A34T

DomainStartEndE-ValueType
transmembrane domain 10 32 N/A INTRINSIC
transmembrane domain 34 51 N/A INTRINSIC
PXA 98 285 9.09e-102 SMART
coiled coil region 293 320 N/A INTRINSIC
RGS 374 514 4.63e-32 SMART
low complexity region 546 562 N/A INTRINSIC
PX 564 677 2.88e-31 SMART
Pfam:Nexin_C 793 903 1.9e-29 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000163677
AA Change: A34T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000130182
Gene: ENSMUSG00000020590
AA Change: A34T

DomainStartEndE-ValueType
transmembrane domain 10 32 N/A INTRINSIC
transmembrane domain 34 51 N/A INTRINSIC
PXA 97 284 9.09e-102 SMART
coiled coil region 292 319 N/A INTRINSIC
RGS 373 513 4.63e-32 SMART
low complexity region 545 561 N/A INTRINSIC
PX 563 676 2.88e-31 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000221272
AA Change: A34T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000222101
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.8%
  • 10x: 94.4%
  • 20x: 86.3%
Validation Efficiency 96% (55/57)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a PHOX domain- and RGS domain-containing protein that belongs to the sorting nexin (SNX) family and the regulator of G protein signaling (RGS) family. The PHOX domain is a phosphoinositide binding domain, and the SNX family members are involved in intracellular trafficking. The RGS family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. The RGS domain of this protein interacts with G alpha(s), accelerates its GTP hydrolysis, and attenuates G alpha(s)-mediated signaling. Overexpression of this protein delayes lysosomal degradation of the epidermal growth factor receptor. Because of its bifunctional role, this protein may link heterotrimeric G protein signaling and vesicular trafficking. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice are growth retarded and die at midgestation with defects in neural tube closure, vasculogenesis and placental development. Mutant visceral yolk sac endoderm cells exhibit altered endocytic compartments, abundant autophagic vacuoles and mislocalization of endocytic markers. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700024G13Rik T C 14: 32,098,588 (GRCm39) E83G possibly damaging Het
Abca9 A G 11: 110,018,273 (GRCm39) S1116P probably damaging Het
Abcc12 T A 8: 87,284,322 (GRCm39) T296S probably damaging Het
Adarb2 A G 13: 8,389,657 (GRCm39) probably benign Het
Arhgef12 C T 9: 42,903,874 (GRCm39) probably benign Het
Asah1 A G 8: 41,807,049 (GRCm39) probably null Het
C1ra A T 6: 124,498,600 (GRCm39) Q431L probably benign Het
C1s2 A T 6: 124,602,453 (GRCm39) I580N probably benign Het
Cacna2d4 C T 6: 119,213,785 (GRCm39) T68I probably benign Het
Car8 A T 4: 8,189,327 (GRCm39) H162Q probably benign Het
Ccdc106 A G 7: 5,062,527 (GRCm39) R116G probably damaging Het
Ccdc136 T A 6: 29,419,376 (GRCm39) N965K probably benign Het
Cd200r3 A G 16: 44,771,910 (GRCm39) E58G possibly damaging Het
Cnksr3 T A 10: 7,076,830 (GRCm39) S121C probably null Het
Cog6 T C 3: 52,916,534 (GRCm39) M212V possibly damaging Het
Ebna1bp2 C A 4: 118,478,269 (GRCm39) probably null Het
Epha1 C A 6: 42,338,385 (GRCm39) M730I probably damaging Het
Fcgbpl1 T C 7: 27,836,582 (GRCm39) F167S probably damaging Het
Fscn2 A T 11: 120,252,848 (GRCm39) E105V probably damaging Het
Gars1 T C 6: 55,030,108 (GRCm39) probably benign Het
Itgb4 G T 11: 115,881,710 (GRCm39) G753V probably damaging Het
Kif23 C T 9: 61,832,084 (GRCm39) V634M probably damaging Het
Krt8 T C 15: 101,907,264 (GRCm39) Y273C possibly damaging Het
Lgmn A G 12: 102,372,151 (GRCm39) probably benign Het
Lrig3 T C 10: 125,845,926 (GRCm39) I785T possibly damaging Het
Lrriq1 A G 10: 103,038,376 (GRCm39) probably benign Het
Lta4h A G 10: 93,316,590 (GRCm39) D491G probably damaging Het
Megf10 A T 18: 57,385,931 (GRCm39) S315C probably damaging Het
Mphosph8 C T 14: 56,905,878 (GRCm39) R24C possibly damaging Het
Neurog2 A G 3: 127,427,490 (GRCm39) D38G possibly damaging Het
Or1j11 G T 2: 36,311,877 (GRCm39) A156S probably benign Het
Or2w2 A T 13: 21,758,457 (GRCm39) Y56* probably null Het
Or2z2 C T 11: 58,346,358 (GRCm39) R139H probably benign Het
Or6b3 T A 1: 92,439,517 (GRCm39) I78F possibly damaging Het
Or8b50 A T 9: 38,518,234 (GRCm39) I158F probably benign Het
Or8g50 T A 9: 39,648,612 (GRCm39) V167D probably benign Het
Pcdhb17 A T 18: 37,619,989 (GRCm39) D593V probably damaging Het
Pde2a G T 7: 101,071,198 (GRCm39) E23* probably null Het
Prex2 G A 1: 11,226,483 (GRCm39) V749I probably benign Het
Ptchd4 A G 17: 42,813,809 (GRCm39) Y570C probably damaging Het
Robo3 C T 9: 37,329,007 (GRCm39) R1237K probably benign Het
Slc6a1 C A 6: 114,284,756 (GRCm39) Y87* probably null Het
Sppl3 T C 5: 115,226,424 (GRCm39) L193P probably damaging Het
Tia1 A T 6: 86,407,321 (GRCm39) Y277F probably benign Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Trappc2l T C 8: 123,342,134 (GRCm39) F127L probably damaging Het
Ushbp1 G T 8: 71,838,663 (GRCm39) Q588K possibly damaging Het
Usp43 T A 11: 67,747,007 (GRCm39) H895L probably benign Het
Vmn1r179 T A 7: 23,628,275 (GRCm39) C155* probably null Het
Vmn2r8 T A 5: 108,945,933 (GRCm39) D558V probably damaging Het
Vps13a T C 19: 16,688,228 (GRCm39) T860A probably benign Het
Vps50 A G 6: 3,565,628 (GRCm39) N522S possibly damaging Het
Zfp180 T C 7: 23,804,643 (GRCm39) F354S probably benign Het
Zgpat A G 2: 181,021,984 (GRCm39) probably benign Het
Other mutations in Snx13
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01011:Snx13 APN 12 35,148,279 (GRCm39) missense probably damaging 1.00
IGL01143:Snx13 APN 12 35,182,159 (GRCm39) missense probably damaging 0.96
IGL01446:Snx13 APN 12 35,174,479 (GRCm39) nonsense probably null
IGL01519:Snx13 APN 12 35,188,471 (GRCm39) unclassified probably benign
IGL01902:Snx13 APN 12 35,183,306 (GRCm39) critical splice acceptor site probably null
IGL01903:Snx13 APN 12 35,135,968 (GRCm39) missense probably benign 0.06
IGL02146:Snx13 APN 12 35,151,078 (GRCm39) missense probably benign 0.00
IGL02175:Snx13 APN 12 35,182,061 (GRCm39) missense possibly damaging 0.83
IGL02197:Snx13 APN 12 35,156,800 (GRCm39) missense probably damaging 1.00
IGL02200:Snx13 APN 12 35,136,884 (GRCm39) missense probably damaging 1.00
IGL02476:Snx13 APN 12 35,136,940 (GRCm39) missense probably damaging 1.00
IGL03171:Snx13 APN 12 35,150,539 (GRCm39) missense probably benign 0.28
resistance UTSW 12 35,162,444 (GRCm39) missense probably damaging 1.00
IGL02835:Snx13 UTSW 12 35,182,126 (GRCm39) missense possibly damaging 0.48
P0042:Snx13 UTSW 12 35,157,541 (GRCm39) missense probably damaging 1.00
R0047:Snx13 UTSW 12 35,151,123 (GRCm39) splice site probably benign
R0047:Snx13 UTSW 12 35,151,123 (GRCm39) splice site probably benign
R0344:Snx13 UTSW 12 35,136,899 (GRCm39) nonsense probably null
R1240:Snx13 UTSW 12 35,141,405 (GRCm39) missense probably damaging 0.99
R1335:Snx13 UTSW 12 35,182,123 (GRCm39) missense probably benign 0.16
R1617:Snx13 UTSW 12 35,136,895 (GRCm39) missense probably damaging 0.99
R2065:Snx13 UTSW 12 35,188,065 (GRCm39) missense possibly damaging 0.91
R2111:Snx13 UTSW 12 35,188,084 (GRCm39) missense probably damaging 1.00
R2385:Snx13 UTSW 12 35,169,792 (GRCm39) missense probably benign 0.36
R2437:Snx13 UTSW 12 35,132,926 (GRCm39) missense probably benign 0.14
R2511:Snx13 UTSW 12 35,188,080 (GRCm39) missense probably benign 0.13
R2860:Snx13 UTSW 12 35,188,116 (GRCm39) missense probably benign 0.45
R2861:Snx13 UTSW 12 35,188,116 (GRCm39) missense probably benign 0.45
R2862:Snx13 UTSW 12 35,188,116 (GRCm39) missense probably benign 0.45
R2992:Snx13 UTSW 12 35,155,190 (GRCm39) missense probably damaging 1.00
R3938:Snx13 UTSW 12 35,194,096 (GRCm39) missense probably benign 0.10
R4304:Snx13 UTSW 12 35,172,941 (GRCm39) missense probably benign 0.10
R4532:Snx13 UTSW 12 35,194,219 (GRCm39) missense probably damaging 0.98
R4692:Snx13 UTSW 12 35,136,917 (GRCm39) missense possibly damaging 0.82
R4783:Snx13 UTSW 12 35,148,285 (GRCm39) missense probably damaging 1.00
R4914:Snx13 UTSW 12 35,182,032 (GRCm39) missense possibly damaging 0.84
R5309:Snx13 UTSW 12 35,194,324 (GRCm39) nonsense probably null
R5425:Snx13 UTSW 12 35,150,643 (GRCm39) nonsense probably null
R5476:Snx13 UTSW 12 35,156,819 (GRCm39) splice site probably null
R5533:Snx13 UTSW 12 35,173,025 (GRCm39) critical splice donor site probably null
R5564:Snx13 UTSW 12 35,174,471 (GRCm39) missense possibly damaging 0.61
R5572:Snx13 UTSW 12 35,153,119 (GRCm39) missense probably damaging 1.00
R5635:Snx13 UTSW 12 35,190,170 (GRCm39) missense probably benign 0.00
R6018:Snx13 UTSW 12 35,097,318 (GRCm39) start gained probably benign
R6612:Snx13 UTSW 12 35,156,758 (GRCm39) missense probably benign 0.19
R6618:Snx13 UTSW 12 35,162,444 (GRCm39) missense probably damaging 1.00
R6737:Snx13 UTSW 12 35,190,185 (GRCm39) missense probably damaging 0.98
R6964:Snx13 UTSW 12 35,169,788 (GRCm39) missense possibly damaging 0.81
R7186:Snx13 UTSW 12 35,142,912 (GRCm39) missense probably damaging 0.99
R7372:Snx13 UTSW 12 35,128,950 (GRCm39) missense probably benign 0.00
R7429:Snx13 UTSW 12 35,183,357 (GRCm39) missense possibly damaging 0.89
R7430:Snx13 UTSW 12 35,183,357 (GRCm39) missense possibly damaging 0.89
R7537:Snx13 UTSW 12 35,135,981 (GRCm39) missense probably damaging 1.00
R7567:Snx13 UTSW 12 35,136,913 (GRCm39) missense probably damaging 1.00
R7582:Snx13 UTSW 12 35,174,534 (GRCm39) nonsense probably null
R7767:Snx13 UTSW 12 35,157,483 (GRCm39) missense probably damaging 1.00
R7771:Snx13 UTSW 12 35,174,527 (GRCm39) missense probably benign
R7838:Snx13 UTSW 12 35,155,174 (GRCm39) missense probably benign 0.26
R7901:Snx13 UTSW 12 35,150,624 (GRCm39) missense probably benign 0.02
R8029:Snx13 UTSW 12 35,169,885 (GRCm39) missense probably damaging 1.00
R8418:Snx13 UTSW 12 35,148,233 (GRCm39) missense probably damaging 1.00
R8961:Snx13 UTSW 12 35,155,285 (GRCm39) missense probably damaging 1.00
R9197:Snx13 UTSW 12 35,155,196 (GRCm39) missense probably benign 0.00
R9372:Snx13 UTSW 12 35,151,048 (GRCm39) missense possibly damaging 0.78
Predicted Primers PCR Primer
(F):5'- ACTATCTCTTATCGCAACTTTGTACTACCACT -3'
(R):5'- AGCTGGCCGCAGTTTACCAAT -3'

Sequencing Primer
(F):5'- GGGAAATTAAAACCTTCTGAAAAGTG -3'
(R):5'- GGCCGCAGTTTACCAATAGATAC -3'
Posted On 2014-03-14