Incidental Mutation 'R1170:Slc6a9'
ID99284
Institutional Source Beutler Lab
Gene Symbol Slc6a9
Ensembl Gene ENSMUSG00000028542
Gene Namesolute carrier family 6 (neurotransmitter transporter, glycine), member 9
SynonymsGlyt1, Glyt-1
MMRRC Submission 039243-MU
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #R1170 (G1)
Quality Score225
Status Validated
Chromosome4
Chromosomal Location117834506-117875198 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to G at 117864806 bp
ZygosityHeterozygous
Amino Acid Change Glutamic Acid to Glycine at position 422 (E422G)
Ref Sequence ENSEMBL: ENSMUSP00000127289 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030269] [ENSMUST00000063857] [ENSMUST00000084325] [ENSMUST00000106422] [ENSMUST00000132043] [ENSMUST00000149168] [ENSMUST00000163288] [ENSMUST00000169885] [ENSMUST00000167287] [ENSMUST00000164853] [ENSMUST00000171052] [ENSMUST00000169990]
Predicted Effect possibly damaging
Transcript: ENSMUST00000030269
AA Change: E418G

PolyPhen 2 Score 0.597 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: E418G

DomainStartEndE-ValueType
Pfam:SNF 27 562 5.1e-234 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000063857
AA Change: E418G

PolyPhen 2 Score 0.597 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: E418G

DomainStartEndE-ValueType
Pfam:SNF 27 562 5.1e-234 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000084325
SMART Domains Protein: ENSMUSP00000081352
Gene: ENSMUSG00000028541

DomainStartEndE-ValueType
transmembrane domain 13 35 N/A INTRINSIC
Pfam:Glyco_transf_7N 94 230 1.9e-47 PFAM
Pfam:Glyco_transf_7C 232 310 2.6e-32 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000106422
SMART Domains Protein: ENSMUSP00000102030
Gene: ENSMUSG00000078588

DomainStartEndE-ValueType
low complexity region 17 46 N/A INTRINSIC
coiled coil region 133 158 N/A INTRINSIC
low complexity region 254 266 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130758
Predicted Effect probably benign
Transcript: ENSMUST00000132043
SMART Domains Protein: ENSMUSP00000122676
Gene: ENSMUSG00000028542

DomainStartEndE-ValueType
Pfam:SNF 32 321 1.4e-132 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000149168
SMART Domains Protein: ENSMUSP00000129359
Gene: ENSMUSG00000028542

DomainStartEndE-ValueType
low complexity region 91 116 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154439
Predicted Effect possibly damaging
Transcript: ENSMUST00000163288
AA Change: E422G

PolyPhen 2 Score 0.767 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: E422G

DomainStartEndE-ValueType
Pfam:SNF 46 566 2.1e-212 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000163974
Predicted Effect noncoding transcript
Transcript: ENSMUST00000164716
Predicted Effect probably benign
Transcript: ENSMUST00000169885
AA Change: E306G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542
AA Change: E306G

DomainStartEndE-ValueType
Pfam:SNF 1 450 1.2e-182 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000167287
SMART Domains Protein: ENSMUSP00000126161
Gene: ENSMUSG00000078588

DomainStartEndE-ValueType
coiled coil region 13 38 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000164853
SMART Domains Protein: ENSMUSP00000132114
Gene: ENSMUSG00000078588

DomainStartEndE-ValueType
low complexity region 17 46 N/A INTRINSIC
coiled coil region 133 158 N/A INTRINSIC
low complexity region 254 266 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000171052
SMART Domains Protein: ENSMUSP00000129502
Gene: ENSMUSG00000078588

DomainStartEndE-ValueType
Pfam:CCDC24 21 201 3.9e-67 PFAM
low complexity region 282 294 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000169990
SMART Domains Protein: ENSMUSP00000127203
Gene: ENSMUSG00000028542

DomainStartEndE-ValueType
Pfam:SNF 84 373 2.3e-132 PFAM
Meta Mutation Damage Score 0.0994 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.4%
  • 20x: 93.0%
Validation Efficiency 100% (105/105)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The amino acid glycine acts as an inhibitory neurotransmitter in the central nervous system. The protein encoded by this gene is one of two transporters that stop glycine signaling by removing it from the synaptic cleft. [provided by RefSeq, Jun 2016]
PHENOTYPE: Homozygous null mice die shortly after birth exhibiting breathing and movement deficiencies. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 104 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700025G04Rik A G 1: 151,980,412 probably benign Het
4932438A13Rik T C 3: 37,044,631 S1136P probably damaging Het
Akap9 G A 5: 4,055,671 S2914N probably benign Het
Alk T C 17: 71,900,734 D1002G probably damaging Het
Ap3d1 A G 10: 80,732,840 probably benign Het
Asb15 T C 6: 24,562,487 probably benign Het
Asxl3 C A 18: 22,524,507 P1858Q probably benign Het
BC003331 T A 1: 150,386,391 E99D probably benign Het
Bud31 T A 5: 145,142,578 probably benign Het
C1qtnf1 G T 11: 118,448,269 R255L probably damaging Het
Cacna2d4 C T 6: 119,307,286 R745W probably damaging Het
Cage1 C T 13: 38,022,880 E330K probably damaging Het
Catsperz T A 19: 6,924,949 N59I probably benign Het
Ccdc110 G T 8: 45,941,885 S271I probably benign Het
Ccdc88b T A 19: 6,853,213 E787V probably damaging Het
Ccna2 A T 3: 36,568,970 probably benign Het
Cd36 T A 5: 17,813,088 D209V probably damaging Het
Cers4 T A 8: 4,519,475 W161R probably damaging Het
Ces2f T A 8: 104,953,546 H442Q probably damaging Het
Chchd6 A C 6: 89,384,687 C245G probably damaging Het
Cndp1 T G 18: 84,611,625 Q481P probably benign Het
Col3a1 A G 1: 45,327,601 R234G unknown Het
Col3a1 A T 1: 45,347,724 N232I probably damaging Het
Colgalt2 A T 1: 152,503,017 D398V probably damaging Het
Cxcl10 TACTCAC TACTCACTCAC 5: 92,348,082 probably null Het
Dcdc2a C A 13: 25,056,307 Q13K probably benign Het
Dzip3 A T 16: 48,961,208 I240N probably damaging Het
Epb41l3 T A 17: 69,259,180 L452* probably null Het
Fam193b C T 13: 55,541,705 A753T probably damaging Het
Fam35a A T 14: 34,268,491 S153T possibly damaging Het
Fam47e G C 5: 92,565,922 probably benign Het
Fastkd1 A G 2: 69,708,649 probably benign Het
Fmnl1 G A 11: 103,197,370 G69D probably benign Het
Foxn2 A G 17: 88,473,666 probably benign Het
Fsip2 A G 2: 82,991,500 E5859G possibly damaging Het
Gm9894 T A 13: 67,764,701 noncoding transcript Het
H2-Bl T C 17: 36,081,091 N44S possibly damaging Het
Helz2 T C 2: 181,229,815 Y2668C probably damaging Het
Hhipl1 T A 12: 108,311,693 C93* probably null Het
Lig1 C T 7: 13,292,153 A278V probably benign Het
Lipn T A 19: 34,071,758 I108K probably benign Het
Lsamp A G 16: 42,151,229 probably benign Het
Map3k14 A G 11: 103,238,917 probably benign Het
Mdm4 A T 1: 132,991,820 C436S probably damaging Het
Mdm4 A G 1: 133,012,692 L33P probably damaging Het
Meiob T C 17: 24,836,484 W422R probably damaging Het
Mppe1 T C 18: 67,227,706 Y254C probably damaging Het
Mterf1a A T 5: 3,890,964 N301K probably benign Het
Muc6 C T 7: 141,644,233 S1210N probably damaging Het
Mycbp2 A T 14: 103,200,152 Y2091* probably null Het
Mylk G A 16: 34,874,039 R156H probably benign Het
Myo15 G T 11: 60,479,407 D998Y probably benign Het
Neb A T 2: 52,196,357 Y5235N probably damaging Het
Nop58 A G 1: 59,704,211 probably benign Het
Nr4a3 A G 4: 48,051,564 H135R probably damaging Het
Nr4a3 A G 4: 48,083,324 K619R probably benign Het
Nrg1 T C 8: 31,837,667 probably benign Het
Olfr1031 A T 2: 85,992,696 N293I probably damaging Het
Olfr1312 A T 2: 112,042,215 D272E probably benign Het
Olfr1484 T C 19: 13,586,213 V260A probably benign Het
Olfr938 T A 9: 39,078,229 D172V possibly damaging Het
Parp3 T C 9: 106,476,005 probably benign Het
Pde2a A G 7: 101,484,543 E103G probably benign Het
Pds5a A T 5: 65,635,302 probably benign Het
Pip4k2c A G 10: 127,211,393 V40A unknown Het
Pitrm1 T C 13: 6,552,744 probably benign Het
Plk4 A G 3: 40,801,847 I64M probably damaging Het
Ppp1r16a C T 15: 76,693,669 Q328* probably null Het
Ppp2r1a T C 17: 20,951,331 probably benign Het
Ppp4r3b T A 11: 29,209,426 N172K probably damaging Het
Prkcg G A 7: 3,319,661 R357Q probably damaging Het
Prmt3 T C 7: 49,848,547 probably null Het
Prx T A 7: 27,518,007 C644* probably null Het
Ptpru A G 4: 131,808,527 probably benign Het
Rbm5 A T 9: 107,742,497 D738E probably damaging Het
Recql5 A T 11: 115,897,234 Y420N probably damaging Het
Rnf17 T C 14: 56,425,631 I152T probably benign Het
Rnpepl1 A G 1: 92,919,195 S580G possibly damaging Het
Ryr3 C T 2: 112,946,987 G275D probably damaging Het
Serpinb9e T A 13: 33,257,752 Y222* probably null Het
Slc10a1 T A 12: 80,956,028 I279F probably damaging Het
Slc12a8 G T 16: 33,662,977 G584V probably damaging Het
Slc35b3 T A 13: 38,937,331 Y311F probably benign Het
Slc44a5 A G 3: 154,257,720 probably null Het
Smpd2 A G 10: 41,488,732 probably null Het
Spast A G 17: 74,381,968 probably null Het
Spink5 A T 18: 43,983,563 E208V probably benign Het
Stag1 T C 9: 100,888,453 probably benign Het
Stambp A G 6: 83,563,821 probably null Het
Sult3a2 A T 10: 33,777,192 M184K possibly damaging Het
Tcp11 T C 17: 28,071,662 D162G probably damaging Het
Themis A C 10: 28,668,748 E30A possibly damaging Het
Tmc7 G A 7: 118,551,260 S350L probably benign Het
Tmem131 A T 1: 36,834,898 Y271* probably null Het
Trim35 T A 14: 66,308,799 S338R probably benign Het
Trim42 C A 9: 97,363,620 V376F probably benign Het
Tshr A T 12: 91,538,097 K11M probably damaging Het
Vps8 A G 16: 21,459,820 probably benign Het
Wdr11 T C 7: 129,607,107 probably benign Het
Wdr26 A T 1: 181,181,294 probably benign Het
Wdtc1 A G 4: 133,297,546 Y447H probably damaging Het
Zfp687 C T 3: 95,008,473 C996Y probably damaging Het
Zfp984 A T 4: 147,755,989 V135E probably benign Het
Zranb2 T C 3: 157,541,865 probably benign Het
Other mutations in Slc6a9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00904:Slc6a9 APN 4 117864617 missense probably damaging 1.00
IGL01728:Slc6a9 APN 4 117864605 missense probably damaging 1.00
IGL02111:Slc6a9 APN 4 117864013 missense probably benign 0.19
R0051:Slc6a9 UTSW 4 117864859 missense probably damaging 1.00
R0051:Slc6a9 UTSW 4 117864859 missense probably damaging 1.00
R2872:Slc6a9 UTSW 4 117849381 start codon destroyed probably null 0.02
R2872:Slc6a9 UTSW 4 117849381 start codon destroyed probably null 0.02
R3499:Slc6a9 UTSW 4 117856803 missense probably benign 0.01
R4744:Slc6a9 UTSW 4 117867895 missense probably benign 0.00
R4970:Slc6a9 UTSW 4 117856008 missense probably damaging 1.00
R5055:Slc6a9 UTSW 4 117868150 splice site probably null
R5103:Slc6a9 UTSW 4 117868155 missense probably benign
R5726:Slc6a9 UTSW 4 117864013 missense probably damaging 1.00
R6836:Slc6a9 UTSW 4 117867886 missense possibly damaging 0.49
R7030:Slc6a9 UTSW 4 117857436 missense possibly damaging 0.94
R7061:Slc6a9 UTSW 4 117868064 missense probably benign 0.40
R7278:Slc6a9 UTSW 4 117868106 missense probably benign 0.31
R7863:Slc6a9 UTSW 4 117864010 missense probably damaging 1.00
R8036:Slc6a9 UTSW 4 117867886 missense possibly damaging 0.49
Z1176:Slc6a9 UTSW 4 117857366 missense probably benign 0.01
Predicted Primers
Posted On2014-01-15