Incidental Mutation 'R5374:Snx6'
ID 428957
Institutional Source Beutler Lab
Gene Symbol Snx6
Ensembl Gene ENSMUSG00000005656
Gene Name sorting nexin 6
Synonyms 2010006G21Rik, 2610032J07Rik, 2810425K19Rik
MMRRC Submission 042950-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.832) question?
Stock # R5374 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 54793124-54842464 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 54817513 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 128 (E128G)
Ref Sequence ENSEMBL: ENSMUSP00000005798 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005798] [ENSMUST00000218934] [ENSMUST00000219781]
AlphaFold Q6P8X1
Predicted Effect probably damaging
Transcript: ENSMUST00000005798
AA Change: E128G

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000005798
Gene: ENSMUSG00000005656
AA Change: E128G

DomainStartEndE-ValueType
Pfam:PX 29 170 2.8e-21 PFAM
Pfam:Vps5 184 399 2e-16 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218066
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218337
Predicted Effect probably benign
Transcript: ENSMUST00000218934
AA Change: E12G

PolyPhen 2 Score 0.296 (Sensitivity: 0.91; Specificity: 0.89)
Predicted Effect probably benign
Transcript: ENSMUST00000219781
Meta Mutation Damage Score 0.2777 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.2%
Validation Efficiency 96% (81/84)
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 sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein associates with the long isoform of the leptin receptor, the transforming growth factor-beta family of receptor serine-threonine kinases, and with receptor tyrosine kinases for platelet-derived growth factor, insulin, and epidermal growth factor. This protein may form oligomeric complexes with family member proteins through interactions of both the PX domain and the coiled coil regions of the molecules. Translocation of this protein from the cytoplasm to the nucleus occurs after binding to proviral integration site 1 protein. This gene results in two transcripts encoding two distinct isoforms. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,773,396 (GRCm39) S862G probably benign Het
Adgrf1 G A 17: 43,601,896 (GRCm39) probably benign Het
Adss2 T G 1: 177,623,954 (GRCm39) I3L probably benign Het
Anapc7 T A 5: 122,576,280 (GRCm39) D302E probably benign Het
Ank3 A G 10: 69,789,306 (GRCm39) probably null Het
Astn2 A C 4: 65,315,242 (GRCm39) V1145G probably damaging Het
Babam2 C T 5: 32,164,574 (GRCm39) probably benign Het
Blvrb A G 7: 27,165,271 (GRCm39) H238R possibly damaging Het
Cacna1b C T 2: 24,596,228 (GRCm39) V488I probably damaging Het
Ccdc88a C T 11: 29,413,409 (GRCm39) T649M possibly damaging Het
Cdh12 A C 15: 21,583,998 (GRCm39) S613R probably damaging Het
Cisd2 A G 3: 135,114,596 (GRCm39) V125A probably benign Het
Clcn2 C A 16: 20,528,419 (GRCm39) G478W possibly damaging Het
Cntnap2 T A 6: 47,084,903 (GRCm39) H1121Q probably benign Het
Corin A T 5: 72,462,296 (GRCm39) C876S probably damaging Het
Cox7c T C 13: 86,194,739 (GRCm39) Y19C probably benign Het
Cplane1 T C 15: 8,300,287 (GRCm39) V3198A unknown Het
Cspp1 T G 1: 10,204,351 (GRCm39) L1038R probably damaging Het
Cwc15 A G 9: 14,416,234 (GRCm39) K147E possibly damaging Het
Dlgap2 A G 8: 14,873,614 (GRCm39) D739G probably benign Het
Dmxl2 A G 9: 54,276,473 (GRCm39) probably benign Het
Dock5 A G 14: 68,043,205 (GRCm39) V864A possibly damaging Het
Dock7 A G 4: 98,877,275 (GRCm39) F1088L possibly damaging Het
Dpysl3 T C 18: 43,494,101 (GRCm39) Y193C probably damaging Het
Dtna T C 18: 23,784,670 (GRCm39) Y730H probably damaging Het
Dusp3 A G 11: 101,875,451 (GRCm39) Y38H possibly damaging Het
Eif3m A T 2: 104,843,277 (GRCm39) I151N probably damaging Het
Entpd2 C T 2: 25,289,738 (GRCm39) T380I probably damaging Het
Epb41l3 C A 17: 69,593,795 (GRCm39) H810N probably damaging Het
Fcrl5 A G 3: 87,353,698 (GRCm39) T348A probably benign Het
Ginm1 A G 10: 7,655,078 (GRCm39) S55P probably damaging Het
Glt1d1 C A 5: 127,734,148 (GRCm39) probably null Het
Gm15433 T A 1: 84,941,833 (GRCm39) noncoding transcript Het
Gm8221 A G 15: 77,510,352 (GRCm39) noncoding transcript Het
Gramd1c A G 16: 43,803,604 (GRCm39) V603A probably benign Het
Grm1 A G 10: 10,956,186 (GRCm39) S33P probably benign Het
Gstp3 T C 19: 4,107,922 (GRCm39) N137S possibly damaging Het
Kdm5d C T Y: 927,995 (GRCm39) P756S probably benign Het
Ly75 A T 2: 60,142,115 (GRCm39) L1332M possibly damaging Het
Med1 T A 11: 98,054,789 (GRCm39) K378N probably damaging Het
Mn1 A G 5: 111,569,752 (GRCm39) probably null Het
Mpo T C 11: 87,694,437 (GRCm39) probably null Het
Nom1 C G 5: 29,646,377 (GRCm39) R555G probably damaging Het
Nsmce4a C T 7: 130,139,900 (GRCm39) R276Q probably benign Het
Nt5c G A 11: 115,381,643 (GRCm39) probably null Het
Olfr908 CACAACAACA CACAACA 9: 38,427,434 (GRCm39) probably benign Het
Or52e18 G T 7: 104,609,203 (GRCm39) H245Q probably damaging Het
Or5p52 T C 7: 107,502,698 (GRCm39) I258T possibly damaging Het
Pcdhga4 T C 18: 37,818,649 (GRCm39) V66A probably damaging Het
Pik3c3 T C 18: 30,445,614 (GRCm39) S534P probably benign Het
Pla2g4e A T 2: 120,016,876 (GRCm39) C222S probably benign Het
Plch1 A C 3: 63,605,499 (GRCm39) H1468Q probably benign Het
Psd2 T A 18: 36,140,556 (GRCm39) W610R probably damaging Het
Ptgs1 A T 2: 36,141,198 (GRCm39) K548N probably damaging Het
Ptprz1 T A 6: 23,007,354 (GRCm39) V1639E probably damaging Het
Rangap1 A T 15: 81,590,695 (GRCm39) S466T probably benign Het
Rgsl1 C T 1: 153,666,053 (GRCm39) V986I probably benign Het
Rhobtb3 T C 13: 76,027,014 (GRCm39) Y453C probably damaging Het
Rspry1 T C 8: 95,349,636 (GRCm39) V8A probably benign Het
Rspry1 C A 8: 95,380,892 (GRCm39) R399S probably benign Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Rxfp2 A G 5: 149,993,725 (GRCm39) T596A probably benign Het
Sap18b G A 8: 96,551,998 (GRCm39) A3T unknown Het
Serpina3j A G 12: 104,280,986 (GRCm39) D53G probably damaging Het
Skint3 T A 4: 112,155,386 (GRCm39) D381E possibly damaging Het
Slirp T C 12: 87,496,192 (GRCm39) S96P possibly damaging Het
Stap1 A G 5: 86,238,787 (GRCm39) T152A possibly damaging Het
Tcf20 A T 15: 82,736,158 (GRCm39) N1764K probably damaging Het
Thap2 A T 10: 115,208,744 (GRCm39) Y125* probably null Het
Ticrr T G 7: 79,340,690 (GRCm39) Y1031* probably null Het
Tnrc18 G A 5: 142,725,911 (GRCm39) R1793C unknown Het
Trpm3 C T 19: 22,903,548 (GRCm39) R945* probably null Het
Ugt1a10 T A 1: 87,983,632 (GRCm39) D143E probably damaging Het
Ush2a C T 1: 188,487,403 (GRCm39) T3057M probably benign Het
Zc3h6 A T 2: 128,844,076 (GRCm39) I207F possibly damaging Het
Zfp518a T C 19: 40,901,954 (GRCm39) S628P probably benign Het
Zup1 T C 10: 33,803,462 (GRCm39) N541D possibly damaging Het
Other mutations in Snx6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01340:Snx6 APN 12 54,801,094 (GRCm39) missense probably damaging 0.99
IGL02682:Snx6 APN 12 54,801,130 (GRCm39) missense probably damaging 1.00
IGL02995:Snx6 APN 12 54,842,295 (GRCm39) splice site probably benign
IGL03240:Snx6 APN 12 54,830,228 (GRCm39) missense probably damaging 0.98
IGL03353:Snx6 APN 12 54,812,469 (GRCm39) splice site probably benign
PIT4362001:Snx6 UTSW 12 54,814,815 (GRCm39) missense possibly damaging 0.80
R0458:Snx6 UTSW 12 54,814,921 (GRCm39) nonsense probably null
R0610:Snx6 UTSW 12 54,798,574 (GRCm39) missense probably damaging 1.00
R0689:Snx6 UTSW 12 54,810,441 (GRCm39) missense probably benign 0.00
R1818:Snx6 UTSW 12 54,830,259 (GRCm39) missense possibly damaging 0.95
R1819:Snx6 UTSW 12 54,830,259 (GRCm39) missense possibly damaging 0.95
R4946:Snx6 UTSW 12 54,817,528 (GRCm39) missense probably damaging 1.00
R5275:Snx6 UTSW 12 54,830,807 (GRCm39) missense probably damaging 1.00
R5373:Snx6 UTSW 12 54,817,513 (GRCm39) missense probably damaging 0.99
R5497:Snx6 UTSW 12 54,803,846 (GRCm39) missense probably damaging 0.98
R5907:Snx6 UTSW 12 54,801,104 (GRCm39) missense probably damaging 1.00
R5947:Snx6 UTSW 12 54,817,549 (GRCm39) nonsense probably null
R6178:Snx6 UTSW 12 54,807,249 (GRCm39) missense probably damaging 0.99
R6287:Snx6 UTSW 12 54,793,813 (GRCm39) missense possibly damaging 0.75
R6321:Snx6 UTSW 12 54,798,798 (GRCm39) missense probably damaging 1.00
R6878:Snx6 UTSW 12 54,810,386 (GRCm39) splice site probably null
R7055:Snx6 UTSW 12 54,830,864 (GRCm39) missense probably damaging 1.00
R8227:Snx6 UTSW 12 54,798,756 (GRCm39) missense possibly damaging 0.82
R8899:Snx6 UTSW 12 54,812,423 (GRCm39) missense probably benign 0.06
R9606:Snx6 UTSW 12 54,814,811 (GRCm39) missense probably benign 0.30
Predicted Primers PCR Primer
(F):5'- TTGCCTTCCTAGTACTTCAATAAGG -3'
(R):5'- TCCTCAGATACCGAGTACAGC -3'

Sequencing Primer
(F):5'- TCCTGAAGAGGCTCTGAT -3'
(R):5'- CCTGGTCTACAAAGTGAGTTCCAG -3'
Posted On 2016-09-06