Incidental Mutation 'R7030:Slc6a9'
ID 546229
Institutional Source Beutler Lab
Gene Symbol Slc6a9
Ensembl Gene ENSMUSG00000028542
Gene Name solute carrier family 6 (neurotransmitter transporter, glycine), member 9
Synonyms Glyt-1, Glyt1
MMRRC Submission 045131-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7030 (G1)
Quality Score 225.009
Status Validated
Chromosome 4
Chromosomal Location 117692240-117726502 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 117714633 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 189 (T189A)
Ref Sequence ENSEMBL: ENSMUSP00000127289 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030269] [ENSMUST00000063857] [ENSMUST00000123994] [ENSMUST00000132043] [ENSMUST00000149168] [ENSMUST00000163288] [ENSMUST00000169885] [ENSMUST00000169990]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000030269
AA Change: T185A

PolyPhen 2 Score 0.864 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: T185A

DomainStartEndE-ValueType
Pfam:SNF 27 562 5.1e-234 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000063857
AA Change: T185A

PolyPhen 2 Score 0.864 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: T185A

DomainStartEndE-ValueType
Pfam:SNF 27 562 5.1e-234 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000123994
SMART Domains Protein: ENSMUSP00000127806
Gene: ENSMUSG00000028542

DomainStartEndE-ValueType
Pfam:SNF 1 114 1.5e-46 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000132043
AA Change: T190A

PolyPhen 2 Score 0.839 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000122676
Gene: ENSMUSG00000028542
AA Change: T190A

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 possibly damaging
Transcript: ENSMUST00000163288
AA Change: T189A

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: T189A

DomainStartEndE-ValueType
Pfam:SNF 46 566 2.1e-212 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000169885
AA Change: T73A

PolyPhen 2 Score 0.245 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542
AA Change: T73A

DomainStartEndE-ValueType
Pfam:SNF 1 450 1.2e-182 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000169990
AA Change: T242A

PolyPhen 2 Score 0.849 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000127203
Gene: ENSMUSG00000028542
AA Change: T242A

DomainStartEndE-ValueType
Pfam:SNF 84 373 2.3e-132 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 98% (92/94)
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: 93 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
AAdacl4fm3 G T 4: 144,430,173 (GRCm39) A272D possibly damaging Het
Abr A T 11: 76,350,038 (GRCm39) I347N probably damaging Het
Acbd4 T A 11: 102,994,985 (GRCm39) L50Q probably damaging Het
Acsl5 T G 19: 55,261,251 (GRCm39) Y69* probably null Het
Agtpbp1 G A 13: 59,652,108 (GRCm39) T401I probably damaging Het
Ap3m2 C T 8: 23,289,807 (GRCm39) E99K probably damaging Het
Arhgef28 A T 13: 98,124,769 (GRCm39) S504R possibly damaging Het
Arsj T A 3: 126,232,752 (GRCm39) D499E probably damaging Het
Bach1 G A 16: 87,516,179 (GRCm39) R240Q probably benign Het
Camk2b T C 11: 5,939,575 (GRCm39) D232G probably damaging Het
Casc3 C T 11: 98,713,359 (GRCm39) P258S possibly damaging Het
Catspere2 T A 1: 177,845,280 (GRCm39) I100N probably damaging Het
Ccdc80 T A 16: 44,943,252 (GRCm39) N787K possibly damaging Het
Celsr1 C A 15: 85,789,679 (GRCm39) C2653F probably damaging Het
Cep170 T C 1: 176,584,051 (GRCm39) E11G probably damaging Het
Chia1 A C 3: 106,022,641 (GRCm39) N12H probably damaging Het
Chrna4 T C 2: 180,671,334 (GRCm39) T141A probably damaging Het
Col25a1 T C 3: 130,272,671 (GRCm39) probably null Het
Dcstamp A T 15: 39,622,929 (GRCm39) I417F probably damaging Het
Dnah5 A G 15: 28,238,738 (GRCm39) I427V probably benign Het
Dnah5 A G 15: 28,333,208 (GRCm39) E2203G probably benign Het
Dnmt3c A T 2: 153,559,345 (GRCm39) S409C probably damaging Het
Dock6 A T 9: 21,724,375 (GRCm39) M1541K probably damaging Het
Dzip1l C T 9: 99,547,888 (GRCm39) T714I probably benign Het
Exoc6b T C 6: 84,825,807 (GRCm39) R535G probably damaging Het
Fam83h A G 15: 75,876,588 (GRCm39) S250P probably benign Het
Fat4 C T 3: 39,036,107 (GRCm39) T3253I probably damaging Het
Fer1l6 T A 15: 58,501,227 (GRCm39) F1302I probably damaging Het
Fmnl1 T G 11: 103,085,600 (GRCm39) probably benign Het
Gckr C A 5: 31,459,554 (GRCm39) F201L possibly damaging Het
Gm10036 A G 18: 15,966,292 (GRCm39) T148A probably benign Het
Gm5142 G A 14: 59,415,909 (GRCm39) S83F probably benign Het
Gpr37 A T 6: 25,689,004 (GRCm39) V31D possibly damaging Het
Gramd2b A T 18: 56,618,321 (GRCm39) Y207F probably damaging Het
Hr T C 14: 70,801,124 (GRCm39) probably null Het
Igf2r A G 17: 12,952,753 (GRCm39) L231P probably damaging Het
Ighv1-66 A T 12: 115,557,157 (GRCm39) W3R probably damaging Het
Insyn2b T A 11: 34,352,030 (GRCm39) V24E probably damaging Het
Kcnu1 T C 8: 26,408,491 (GRCm39) S101P probably benign Het
Klhl23 T G 2: 69,664,310 (GRCm39) V553G probably damaging Het
Lrp1 T C 10: 127,388,745 (GRCm39) I3235V probably damaging Het
Mb A T 15: 76,900,256 (GRCm39) I57N probably damaging Het
Micu1 T C 10: 59,624,843 (GRCm39) I295T possibly damaging Het
Mink1 G A 11: 70,498,601 (GRCm39) V589I possibly damaging Het
Mndal T C 1: 173,703,160 (GRCm39) K82E probably damaging Het
Mroh1 A C 15: 76,321,517 (GRCm39) K1066T probably benign Het
Muc5b T A 7: 141,396,192 (GRCm39) N149K unknown Het
Myo7b G T 18: 32,104,626 (GRCm39) L1404I probably damaging Het
Nlrc4 A G 17: 74,753,001 (GRCm39) S461P probably damaging Het
Nudt12 A T 17: 59,310,348 (GRCm39) D418E probably benign Het
Or2g7 T A 17: 38,378,948 (GRCm39) D295E probably benign Het
Or5g27 G T 2: 85,409,746 (GRCm39) R54S possibly damaging Het
Pcdha1 A G 18: 37,292,326 (GRCm39) H817R probably damaging Het
Pcdha4 A G 18: 37,087,080 (GRCm39) Y421C probably damaging Het
Pcf11 T C 7: 92,306,886 (GRCm39) D1094G probably benign Het
Pck2 A T 14: 55,785,223 (GRCm39) D427V probably damaging Het
Pclo A G 5: 14,726,421 (GRCm39) T1760A probably benign Het
Pdzk1ip1 T A 4: 114,950,188 (GRCm39) Y83N probably damaging Het
Pgs1 T C 11: 117,893,312 (GRCm39) I213T probably damaging Het
Plin4 T A 17: 56,410,969 (GRCm39) T1021S probably damaging Het
Plxnb1 T A 9: 108,941,375 (GRCm39) I1677N probably damaging Het
Pm20d2 T C 4: 33,174,752 (GRCm39) E378G possibly damaging Het
Prkcq T G 2: 11,231,661 (GRCm39) probably null Het
Psmd2 C T 16: 20,480,883 (GRCm39) P780L probably damaging Het
Pvr A G 7: 19,639,105 (GRCm39) S392P possibly damaging Het
Rad51ap2 G C 12: 11,507,432 (GRCm39) L451F possibly damaging Het
Rbm20 A G 19: 53,823,197 (GRCm39) E598G probably damaging Het
Rho A T 6: 115,912,504 (GRCm39) N123Y possibly damaging Het
Rictor T C 15: 6,737,934 (GRCm39) probably null Het
Rilpl2 T G 5: 124,606,656 (GRCm39) K186T probably damaging Het
Rps6ka4 A C 19: 6,816,992 (GRCm39) L61R probably damaging Het
Sds C A 5: 120,618,890 (GRCm39) Q118K probably benign Het
Septin1 C T 7: 126,816,157 (GRCm39) R91K probably benign Het
Sf3a3 A G 4: 124,616,673 (GRCm39) Y185C probably damaging Het
Shtn1 T C 19: 58,998,266 (GRCm39) M376V possibly damaging Het
Slc7a6 T G 8: 106,922,606 (GRCm39) V464G possibly damaging Het
Smg8 T A 11: 86,975,919 (GRCm39) D554V probably damaging Het
Sox8 A G 17: 25,789,082 (GRCm39) probably null Het
Spata31e4 G T 13: 50,857,019 (GRCm39) V886L possibly damaging Het
Spats2l T A 1: 57,918,689 (GRCm39) V41D probably damaging Het
Sult2a3 A T 7: 13,801,493 (GRCm39) F282Y probably damaging Het
Svs3a T G 2: 164,132,091 (GRCm39) Y220D probably damaging Het
Teddm1a T A 1: 153,768,369 (GRCm39) Y278N probably damaging Het
Tlk1 T C 2: 70,552,272 (GRCm39) Y526C probably damaging Het
Tmc3 T A 7: 83,266,025 (GRCm39) probably null Het
Ttn T A 2: 76,596,583 (GRCm39) E20110V probably damaging Het
Tulp4 A G 17: 6,264,941 (GRCm39) D235G probably damaging Het
Usp50 T C 2: 126,622,395 (GRCm39) Y55C possibly damaging Het
Vmn1r224 T C 17: 20,639,789 (GRCm39) L122P probably benign Het
Vmn2r62 A G 7: 42,438,473 (GRCm39) L121P possibly damaging Het
Whrn G T 4: 63,413,368 (GRCm39) probably benign Het
Zer1 G T 2: 30,001,033 (GRCm39) H129Q probably benign Het
Zfand4 G A 6: 116,282,618 (GRCm39) A64T probably benign Het
Other mutations in Slc6a9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00904:Slc6a9 APN 4 117,721,814 (GRCm39) missense probably damaging 1.00
IGL01728:Slc6a9 APN 4 117,721,802 (GRCm39) missense probably damaging 1.00
IGL02111:Slc6a9 APN 4 117,721,210 (GRCm39) missense probably benign 0.19
R0051:Slc6a9 UTSW 4 117,722,056 (GRCm39) missense probably damaging 1.00
R0051:Slc6a9 UTSW 4 117,722,056 (GRCm39) missense probably damaging 1.00
R1170:Slc6a9 UTSW 4 117,722,003 (GRCm39) missense possibly damaging 0.77
R2872:Slc6a9 UTSW 4 117,706,578 (GRCm39) start codon destroyed probably null 0.02
R2872:Slc6a9 UTSW 4 117,706,578 (GRCm39) start codon destroyed probably null 0.02
R3499:Slc6a9 UTSW 4 117,714,000 (GRCm39) missense probably benign 0.01
R4744:Slc6a9 UTSW 4 117,725,092 (GRCm39) missense probably benign 0.00
R4970:Slc6a9 UTSW 4 117,713,205 (GRCm39) missense probably damaging 1.00
R5055:Slc6a9 UTSW 4 117,725,347 (GRCm39) splice site probably null
R5103:Slc6a9 UTSW 4 117,725,352 (GRCm39) missense probably benign
R5726:Slc6a9 UTSW 4 117,721,210 (GRCm39) missense probably damaging 1.00
R6836:Slc6a9 UTSW 4 117,725,083 (GRCm39) missense possibly damaging 0.49
R7061:Slc6a9 UTSW 4 117,725,261 (GRCm39) missense probably benign 0.40
R7278:Slc6a9 UTSW 4 117,725,303 (GRCm39) missense probably benign 0.31
R7863:Slc6a9 UTSW 4 117,721,207 (GRCm39) missense probably damaging 1.00
R8036:Slc6a9 UTSW 4 117,725,083 (GRCm39) missense possibly damaging 0.49
R8722:Slc6a9 UTSW 4 117,714,452 (GRCm39) missense unknown
R9302:Slc6a9 UTSW 4 117,706,596 (GRCm39) missense possibly damaging 0.91
R9575:Slc6a9 UTSW 4 117,714,603 (GRCm39) missense probably benign
R9627:Slc6a9 UTSW 4 117,721,210 (GRCm39) missense probably damaging 1.00
R9749:Slc6a9 UTSW 4 117,721,198 (GRCm39) missense probably damaging 0.98
Z1176:Slc6a9 UTSW 4 117,714,563 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- CAACGTGGTCATCTGCATCG -3'
(R):5'- CGTCTACTGTTACGCCGTAAG -3'

Sequencing Primer
(F):5'- GTGGTCATCTGCATCGCCTTC -3'
(R):5'- GTAAGGACTCCCAGTTCACCTC -3'
Posted On 2019-05-13