Incidental Mutation 'R1876:Slc6a4'
ID 211254
Institutional Source Beutler Lab
Gene Symbol Slc6a4
Ensembl Gene ENSMUSG00000020838
Gene Name solute carrier family 6 (neurotransmitter transporter, serotonin), member 4
Synonyms 5-HTT, Htt, Sert
MMRRC Submission 039898-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.335) question?
Stock # R1876 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 76889429-76923166 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 76905990 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 264 (T264S)
Ref Sequence ENSEMBL: ENSMUSP00000104039 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021195] [ENSMUST00000108402] [ENSMUST00000129572]
AlphaFold Q60857
Predicted Effect probably benign
Transcript: ENSMUST00000021195
AA Change: T264S

PolyPhen 2 Score 0.337 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000021195
Gene: ENSMUSG00000020838
AA Change: T264S

DomainStartEndE-ValueType
Pfam:5HT_transport_N 24 64 3e-27 PFAM
Pfam:SNF 79 600 7.3e-232 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000108402
AA Change: T264S

PolyPhen 2 Score 0.337 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000104039
Gene: ENSMUSG00000020838
AA Change: T264S

DomainStartEndE-ValueType
Pfam:5HT_transporter 23 64 7.8e-30 PFAM
Pfam:SNF 79 600 7.3e-232 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000129572
SMART Domains Protein: ENSMUSP00000115264
Gene: ENSMUSG00000020838

DomainStartEndE-ValueType
Pfam:5HT_transporter 23 64 1e-30 PFAM
Pfam:SNF 79 158 1.8e-46 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137819
Meta Mutation Damage Score 0.1961 question?
Coding Region Coverage
  • 1x: 97.3%
  • 3x: 96.7%
  • 10x: 95.1%
  • 20x: 92.2%
Validation Efficiency 99% (82/83)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an integral membrane protein that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The encoded protein terminates the action of serotonin and recycles it in a sodium-dependent manner. This protein is a target of psychomotor stimulants, such as amphetamines and cocaine, and is a member of the sodium:neurotransmitter symporter family. A repeat length polymorphism in the promoter of this gene has been shown to affect the rate of serotonin uptake and may play a role in sudden infant death syndrome, aggressive behavior in Alzheimer disease patients, and depression-susceptibility in people experiencing emotional trauma. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit greatly diminished brain serotonin levels and lack cortical barrel patterns. Also, mutants lack the locomotor enhancing response to the drug (+)-3,4-methylenedioxymethamphetamine. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aasdh C A 5: 77,025,396 (GRCm39) C961F probably damaging Het
Abca16 A C 7: 120,032,608 (GRCm39) D209A probably damaging Het
Adamts14 T C 10: 61,036,151 (GRCm39) I1047V probably benign Het
Ak1 A G 2: 32,520,282 (GRCm39) K27E probably damaging Het
Akap9 T A 5: 4,011,809 (GRCm39) D837E probably benign Het
Arfgef3 T C 10: 18,473,104 (GRCm39) Y1653C probably damaging Het
Atad2 T G 15: 57,970,264 (GRCm39) I446L probably benign Het
Atp8b3 T G 10: 80,365,912 (GRCm39) T313P possibly damaging Het
Btg4 T C 9: 51,028,489 (GRCm39) L72S probably damaging Het
Canx A G 11: 50,195,186 (GRCm39) I294T probably damaging Het
Casp1 G A 9: 5,303,663 (GRCm39) E250K probably benign Het
Chchd10 T A 10: 75,772,166 (GRCm39) S46T probably benign Het
Col12a1 G T 9: 79,585,563 (GRCm39) Y1271* probably null Het
Col3a1 G A 1: 45,381,395 (GRCm39) probably null Het
Ctc1 A T 11: 68,922,390 (GRCm39) T872S probably benign Het
Cx3cl1 T C 8: 95,507,048 (GRCm39) F351S probably damaging Het
Cyb5r4 T A 9: 86,937,867 (GRCm39) H295Q probably damaging Het
Cyp2j7 T C 4: 96,105,656 (GRCm39) T285A probably benign Het
Dip2a G A 10: 76,153,925 (GRCm39) T135M probably damaging Het
Eif1ad18 T G 12: 88,050,810 (GRCm39) I115S probably damaging Het
Fgf10 A G 13: 118,925,695 (GRCm39) E158G probably damaging Het
Ftcd G T 10: 76,417,403 (GRCm39) A281S probably benign Het
Gpat4 A T 8: 23,669,486 (GRCm39) M333K possibly damaging Het
Gpcpd1 A G 2: 132,376,673 (GRCm39) L541P probably damaging Het
Grk5 T C 19: 61,071,663 (GRCm39) Y408H probably damaging Het
Hcrtr2 A G 9: 76,153,627 (GRCm39) probably null Het
Hsd17b13 T A 5: 104,116,633 (GRCm39) N127I probably damaging Het
Hspa4 T G 11: 53,174,983 (GRCm39) D158A probably benign Het
Ice2 G A 9: 69,322,857 (GRCm39) A451T possibly damaging Het
Inpp5e A T 2: 26,298,169 (GRCm39) I144K possibly damaging Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Lrrc49 T C 9: 60,495,060 (GRCm39) I652V possibly damaging Het
Man1a A T 10: 53,795,268 (GRCm39) W571R probably damaging Het
Mecom A G 3: 30,047,807 (GRCm39) S32P probably damaging Het
Mrpl40 A G 16: 18,691,224 (GRCm39) I162T probably benign Het
Mslnl G A 17: 25,961,908 (GRCm39) V128M probably damaging Het
Mtmr12 T C 15: 12,257,716 (GRCm39) W265R probably damaging Het
Mup21 C T 4: 62,067,663 (GRCm39) V79I probably benign Het
Myh11 G A 16: 14,086,967 (GRCm39) probably benign Het
Myom3 T A 4: 135,506,711 (GRCm39) F495I probably benign Het
Ncoa7 A T 10: 30,574,122 (GRCm39) probably benign Het
Nisch T C 14: 30,895,594 (GRCm39) Y45C probably damaging Het
Nkain2 T A 10: 32,766,435 (GRCm39) probably benign Het
Or1ak2 A T 2: 36,827,775 (GRCm39) I215F possibly damaging Het
Or4k1 A G 14: 50,377,629 (GRCm39) S156P probably damaging Het
Pdcl A C 2: 37,245,708 (GRCm39) H98Q probably damaging Het
Pink1 A G 4: 138,043,013 (GRCm39) V427A probably damaging Het
Plce1 T C 19: 38,769,067 (GRCm39) S2242P probably damaging Het
Plrg1 C A 3: 82,976,375 (GRCm39) probably benign Het
Plxnc1 A G 10: 94,702,803 (GRCm39) F586S possibly damaging Het
Pnpla7 G A 2: 24,930,985 (GRCm39) V867M possibly damaging Het
Ppfia3 T A 7: 45,001,631 (GRCm39) D427V possibly damaging Het
Ppp6r3 A T 19: 3,521,971 (GRCm39) probably benign Het
Pros1 A T 16: 62,723,881 (GRCm39) S210C probably damaging Het
Ptk2b A G 14: 66,395,841 (GRCm39) S839P probably benign Het
Ptpre T C 7: 135,280,046 (GRCm39) V570A possibly damaging Het
Rbm48 C T 5: 3,645,259 (GRCm39) A142T probably damaging Het
Safb2 T C 17: 56,883,909 (GRCm39) probably null Het
Scnn1a A G 6: 125,315,801 (GRCm39) E384G probably benign Het
Sec23ip A G 7: 128,354,575 (GRCm39) Y277C probably benign Het
Slc25a29 G A 12: 108,793,637 (GRCm39) T42M probably damaging Het
Srgap3 A G 6: 112,752,527 (GRCm39) M319T probably damaging Het
Strn4 T A 7: 16,572,207 (GRCm39) I640N probably damaging Het
Tacc2 A G 7: 130,225,475 (GRCm39) D739G probably benign Het
Tigd4 T A 3: 84,501,242 (GRCm39) L53* probably null Het
Tlr6 T A 5: 65,112,763 (GRCm39) D48V probably damaging Het
Tmem125 T C 4: 118,399,101 (GRCm39) D110G probably damaging Het
Tmem198 A G 1: 75,461,567 (GRCm39) D341G probably damaging Het
Tnfaip3 A G 10: 18,880,682 (GRCm39) F462L possibly damaging Het
Tnrc6a CTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTT CTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTT 7: 122,761,669 (GRCm39) probably benign Het
Ush2a T A 1: 188,410,486 (GRCm39) I2378N possibly damaging Het
Usp47 A G 7: 111,654,127 (GRCm39) T108A probably damaging Het
Vmn1r236 T A 17: 21,506,900 (GRCm39) I6K probably benign Het
Vmn2r65 A T 7: 84,595,505 (GRCm39) V393D probably damaging Het
Other mutations in Slc6a4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00900:Slc6a4 APN 11 76,914,006 (GRCm39) missense probably benign 0.00
IGL01403:Slc6a4 APN 11 76,922,498 (GRCm39) missense probably benign 0.00
IGL01608:Slc6a4 APN 11 76,917,961 (GRCm39) missense probably damaging 1.00
IGL01759:Slc6a4 APN 11 76,904,114 (GRCm39) missense probably damaging 1.00
IGL02239:Slc6a4 APN 11 76,917,982 (GRCm39) missense probably benign 0.01
IGL02491:Slc6a4 APN 11 76,918,034 (GRCm39) missense probably damaging 1.00
IGL03221:Slc6a4 APN 11 76,917,931 (GRCm39) missense probably benign
R1122:Slc6a4 UTSW 11 76,918,012 (GRCm39) missense possibly damaging 0.90
R1574:Slc6a4 UTSW 11 76,910,022 (GRCm39) missense possibly damaging 0.93
R1574:Slc6a4 UTSW 11 76,910,022 (GRCm39) missense possibly damaging 0.93
R1768:Slc6a4 UTSW 11 76,904,078 (GRCm39) missense probably damaging 1.00
R1884:Slc6a4 UTSW 11 76,904,201 (GRCm39) missense probably benign 0.01
R4362:Slc6a4 UTSW 11 76,907,904 (GRCm39) missense probably damaging 1.00
R4595:Slc6a4 UTSW 11 76,910,689 (GRCm39) missense probably benign 0.16
R4855:Slc6a4 UTSW 11 76,904,135 (GRCm39) missense probably damaging 1.00
R5569:Slc6a4 UTSW 11 76,914,081 (GRCm39) missense possibly damaging 0.88
R5747:Slc6a4 UTSW 11 76,901,337 (GRCm39) missense probably damaging 0.97
R5802:Slc6a4 UTSW 11 76,910,062 (GRCm39) missense probably damaging 1.00
R6242:Slc6a4 UTSW 11 76,909,184 (GRCm39) nonsense probably null
R6344:Slc6a4 UTSW 11 76,909,080 (GRCm39) missense probably damaging 1.00
R6443:Slc6a4 UTSW 11 76,914,027 (GRCm39) missense probably benign 0.05
R6935:Slc6a4 UTSW 11 76,917,994 (GRCm39) missense probably benign 0.06
R7283:Slc6a4 UTSW 11 76,901,522 (GRCm39) missense probably benign
R7313:Slc6a4 UTSW 11 76,901,527 (GRCm39) missense possibly damaging 0.75
R7347:Slc6a4 UTSW 11 76,907,911 (GRCm39) nonsense probably null
R7535:Slc6a4 UTSW 11 76,905,976 (GRCm39) missense possibly damaging 0.70
R7826:Slc6a4 UTSW 11 76,903,851 (GRCm39) missense probably benign 0.27
R8055:Slc6a4 UTSW 11 76,901,424 (GRCm39) missense probably benign 0.00
R9296:Slc6a4 UTSW 11 76,909,110 (GRCm39) missense probably benign 0.19
R9325:Slc6a4 UTSW 11 76,909,999 (GRCm39) missense probably benign 0.13
RF007:Slc6a4 UTSW 11 76,910,008 (GRCm39) missense probably damaging 1.00
Z1177:Slc6a4 UTSW 11 76,907,509 (GRCm39) frame shift probably null
Z1186:Slc6a4 UTSW 11 76,903,858 (GRCm39) missense probably benign
Z1186:Slc6a4 UTSW 11 76,901,382 (GRCm39) missense probably benign
Z1187:Slc6a4 UTSW 11 76,903,858 (GRCm39) missense probably benign
Z1187:Slc6a4 UTSW 11 76,901,382 (GRCm39) missense probably benign
Z1188:Slc6a4 UTSW 11 76,903,858 (GRCm39) missense probably benign
Z1188:Slc6a4 UTSW 11 76,901,382 (GRCm39) missense probably benign
Z1189:Slc6a4 UTSW 11 76,903,858 (GRCm39) missense probably benign
Z1189:Slc6a4 UTSW 11 76,901,382 (GRCm39) missense probably benign
Z1190:Slc6a4 UTSW 11 76,903,858 (GRCm39) missense probably benign
Z1190:Slc6a4 UTSW 11 76,901,382 (GRCm39) missense probably benign
Z1192:Slc6a4 UTSW 11 76,903,858 (GRCm39) missense probably benign
Z1192:Slc6a4 UTSW 11 76,901,382 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- CCAGTGAATTTGCAGCTTGTTC -3'
(R):5'- TATCACAGGATGAACGTGTTTGG -3'

Sequencing Primer
(F):5'- TTCAGGATGAGTGAGCCCCATTC -3'
(R):5'- CTACTCAGTAGCCATCTTGAG -3'
Posted On 2014-06-30