Incidental Mutation 'R1474:Tmed5'
ID 163889
Institutional Source Beutler Lab
Gene Symbol Tmed5
Ensembl Gene ENSMUSG00000063406
Gene Name transmembrane p24 trafficking protein 5
Synonyms 4432412D15Rik, 3110020O18Rik
MMRRC Submission 039527-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.129) question?
Stock # R1474 (G1)
Quality Score 144
Status Validated
Chromosome 5
Chromosomal Location 108269422-108280486 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 108280248 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 15 (S15T)
Ref Sequence ENSEMBL: ENSMUSP00000056449 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002837] [ENSMUST00000047677] [ENSMUST00000061203] [ENSMUST00000117759] [ENSMUST00000118036] [ENSMUST00000119437] [ENSMUST00000119784] [ENSMUST00000197718]
AlphaFold Q9CXE7
Predicted Effect probably benign
Transcript: ENSMUST00000002837
AA Change: S15T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000002837
Gene: ENSMUSG00000063406
AA Change: S15T

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
EMP24_GP25L 35 222 5e-58 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000047677
SMART Domains Protein: ENSMUSP00000036507
Gene: ENSMUSG00000056531

DomainStartEndE-ValueType
coiled coil region 109 140 N/A INTRINSIC
coiled coil region 168 320 N/A INTRINSIC
coiled coil region 344 405 N/A INTRINSIC
coiled coil region 507 1307 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000061203
AA Change: S15T

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000056449
Gene: ENSMUSG00000063406
AA Change: S15T

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
Pfam:EMP24_GP25L 35 112 4.2e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000117759
AA Change: S15T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000112612
Gene: ENSMUSG00000063406
AA Change: S15T

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
Pfam:EMP24_GP25L 35 100 4.9e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000118036
AA Change: S15T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000113922
Gene: ENSMUSG00000063406
AA Change: S15T

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
Pfam:EMP24_GP25L 35 99 1.6e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000119437
AA Change: S15T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000112406
Gene: ENSMUSG00000063406
AA Change: S15T

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
EMP24_GP25L 35 160 9.65e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000119784
AA Change: S15T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000113422
Gene: ENSMUSG00000063406
AA Change: S15T

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
Pfam:EMP24_GP25L 35 96 2.4e-14 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200463
Predicted Effect probably benign
Transcript: ENSMUST00000197718
SMART Domains Protein: ENSMUSP00000142963
Gene: ENSMUSG00000056531

DomainStartEndE-ValueType
coiled coil region 109 140 N/A INTRINSIC
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.6%
Validation Efficiency 95% (104/110)
Allele List at MGI
Other mutations in this stock
Total: 106 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8a C A 11: 109,960,635 (GRCm39) A628S probably damaging Het
Abca9 T C 11: 110,036,405 (GRCm39) N568S probably damaging Het
Ada C T 2: 163,574,814 (GRCm39) A108T possibly damaging Het
Adam6a T A 12: 113,508,069 (GRCm39) D147E possibly damaging Het
Ampd1 A T 3: 103,006,154 (GRCm39) T655S probably damaging Het
Ankk1 A G 9: 49,327,139 (GRCm39) F680S probably damaging Het
Asap1 G A 15: 63,991,869 (GRCm39) T783I probably benign Het
Astn1 T A 1: 158,329,923 (GRCm39) N259K probably damaging Het
Birc6 T C 17: 74,886,673 (GRCm39) V667A probably damaging Het
Brat1 G A 5: 140,698,382 (GRCm39) V185I probably benign Het
Btnl6 T C 17: 34,732,620 (GRCm39) Y318C probably damaging Het
Caskin2 G A 11: 115,694,522 (GRCm39) P360S probably benign Het
Ccdc121rt3 T C 5: 112,503,642 (GRCm39) T21A probably benign Het
Cd68 T A 11: 69,555,754 (GRCm39) probably benign Het
Cdca2 T C 14: 67,952,355 (GRCm39) probably benign Het
Cdk6 G A 5: 3,523,217 (GRCm39) M212I probably benign Het
Ceacam5 T A 7: 17,481,159 (GRCm39) F302Y probably damaging Het
Celsr2 T C 3: 108,301,055 (GRCm39) E2746G possibly damaging Het
Clec4a4 G A 6: 122,989,703 (GRCm39) V115I probably benign Het
Clip3 C A 7: 29,998,307 (GRCm39) A251E possibly damaging Het
Cmah T C 13: 24,623,180 (GRCm39) L350P probably damaging Het
Cntnap5a C T 1: 116,370,103 (GRCm39) R907* probably null Het
Cntnap5b T C 1: 99,999,814 (GRCm39) Y191H probably benign Het
Col4a4 A T 1: 82,458,207 (GRCm39) C1122* probably null Het
Coq5 A G 5: 115,433,842 (GRCm39) probably benign Het
Cpxcr1 A G X: 115,387,136 (GRCm39) K16E possibly damaging Het
Dclk3 T C 9: 111,298,304 (GRCm39) I616T probably benign Het
Dhrs3 A T 4: 144,646,057 (GRCm39) T122S probably damaging Het
Dnm1 T C 2: 32,210,596 (GRCm39) I502V probably benign Het
Dscaml1 G T 9: 45,596,519 (GRCm39) G788W probably damaging Het
Dusp10 C T 1: 183,769,645 (GRCm39) probably null Het
Ehbp1l1 C A 19: 5,769,112 (GRCm39) L730F possibly damaging Het
Eif2ak1 C T 5: 143,808,785 (GRCm39) H75Y probably damaging Het
Evi2a T C 11: 79,418,398 (GRCm39) T71A probably benign Het
Fam184a A T 10: 53,511,461 (GRCm39) S1073T probably damaging Het
Fam227a T C 15: 79,499,582 (GRCm39) Y591C probably damaging Het
Fam83a C T 15: 57,873,272 (GRCm39) T367M probably benign Het
Fam83g A G 11: 61,593,819 (GRCm39) D451G probably damaging Het
Fbn1 A G 2: 125,203,185 (GRCm39) F1213L possibly damaging Het
Fcgbp G A 7: 27,791,273 (GRCm39) V845I probably benign Het
Fermt1 C T 2: 132,766,942 (GRCm39) E342K probably benign Het
Foxn1 T A 11: 78,251,933 (GRCm39) M433L probably benign Het
Gm6632 T G 5: 59,211,679 (GRCm39) noncoding transcript Het
Gnl3 A T 14: 30,738,418 (GRCm39) probably benign Het
Hhipl1 C T 12: 108,277,996 (GRCm39) T108I probably damaging Het
Hs2st1 A T 3: 144,141,256 (GRCm39) F271I possibly damaging Het
Ido1 T C 8: 25,074,462 (GRCm39) S303G probably damaging Het
Ints2 C T 11: 86,117,607 (GRCm39) R705H probably damaging Het
Kcnc2 A G 10: 112,292,305 (GRCm39) K49E probably damaging Het
Kif3b T A 2: 153,162,235 (GRCm39) V482E probably damaging Het
Ldlrad2 G A 4: 137,299,525 (GRCm39) P100S probably benign Het
Lrba G T 3: 86,687,573 (GRCm39) probably benign Het
Lsm11 A T 11: 45,824,730 (GRCm39) W266R probably benign Het
Mob3a A T 10: 80,522,988 (GRCm39) M215K probably benign Het
Mterf1b T G 5: 4,247,163 (GRCm39) L268R probably damaging Het
Mvk T C 5: 114,598,157 (GRCm39) F365L probably damaging Het
Myo16 T A 8: 10,552,796 (GRCm39) F945I probably damaging Het
Myo1f G T 17: 33,813,001 (GRCm39) K602N possibly damaging Het
Nr2c2ap A T 8: 70,585,765 (GRCm39) M108L probably benign Het
Ofcc1 C T 13: 40,362,305 (GRCm39) G206R probably benign Het
Ogfrl1 A G 1: 23,414,890 (GRCm39) F206L probably damaging Het
Ola1 A T 2: 72,987,188 (GRCm39) I148N probably damaging Het
Or14c46 G T 7: 85,918,270 (GRCm39) H242Q probably damaging Het
Or4d10b T A 19: 12,036,844 (GRCm39) T91S probably benign Het
Or51f1d A G 7: 102,701,288 (GRCm39) Y261C probably damaging Het
Or6c2 A T 10: 129,362,824 (GRCm39) M243L probably benign Het
Or9m2 A G 2: 87,821,334 (GRCm39) N293S probably damaging Het
Otof A G 5: 30,536,876 (GRCm39) probably null Het
Pah G T 10: 87,414,175 (GRCm39) K341N probably damaging Het
Pfdn5 T A 15: 102,236,946 (GRCm39) probably null Het
Piezo2 A G 18: 63,216,202 (GRCm39) C960R probably damaging Het
Pitx2 T C 3: 129,012,488 (GRCm39) V306A probably damaging Het
Pkd1l2 C A 8: 117,792,236 (GRCm39) probably benign Het
Plekho1 T C 3: 95,896,878 (GRCm39) E197G probably damaging Het
Polr2i A G 7: 29,932,227 (GRCm39) N34S probably damaging Het
Psph A T 5: 129,848,614 (GRCm39) D22E probably damaging Het
Ptprs C A 17: 56,731,128 (GRCm39) A687S probably damaging Het
Ralgapa1 T C 12: 55,788,265 (GRCm39) K606R probably benign Het
Rigi A G 4: 40,208,868 (GRCm39) V703A possibly damaging Het
Rims1 A G 1: 22,577,362 (GRCm39) probably benign Het
Rnf213 C T 11: 119,328,576 (GRCm39) P2002L probably damaging Het
Ryr3 A T 2: 112,740,307 (GRCm39) C555S probably damaging Het
Sftpd C A 14: 40,894,384 (GRCm39) G345V probably damaging Het
Slc41a1 T A 1: 131,774,319 (GRCm39) M462K probably damaging Het
Slc44a2 A G 9: 21,264,990 (GRCm39) E676G probably damaging Het
Sox6 T A 7: 115,300,926 (GRCm39) probably benign Het
Spdye4b G A 5: 143,181,472 (GRCm39) R109Q probably damaging Het
Spef1l C A 7: 139,556,555 (GRCm39) R144L probably benign Het
Spink8 A T 9: 109,649,706 (GRCm39) I63L probably damaging Het
St3gal3 A G 4: 117,871,983 (GRCm39) L73P probably damaging Het
Stab1 A G 14: 30,871,818 (GRCm39) L1247P probably benign Het
Tat A G 8: 110,718,195 (GRCm39) R27G probably benign Het
Tcerg1l C T 7: 137,881,804 (GRCm39) R295H probably damaging Het
Tfrc T C 16: 32,445,467 (GRCm39) V596A probably damaging Het
Tgfb3 C T 12: 86,116,120 (GRCm39) probably null Het
Tph1 A T 7: 46,303,286 (GRCm39) S231T probably benign Het
Trim30d G A 7: 104,121,701 (GRCm39) S198L probably damaging Het
Trpm6 T C 19: 18,773,859 (GRCm39) M412T probably benign Het
Ttn G T 2: 76,612,589 (GRCm39) D15417E probably benign Het
U2surp A G 9: 95,375,251 (GRCm39) I157T possibly damaging Het
Ubr4 A G 4: 139,156,890 (GRCm39) D2305G probably damaging Het
Uvssa A G 5: 33,546,165 (GRCm39) K179E probably benign Het
Vps35l T C 7: 118,359,436 (GRCm39) F230S probably damaging Het
Xirp2 A G 2: 67,355,411 (GRCm39) K3391E probably benign Het
Xpo7 T A 14: 70,936,473 (GRCm39) H170L probably benign Het
Zrsr2-ps1 T C 11: 22,924,404 (GRCm39) W393R probably benign Het
Other mutations in Tmed5
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02457:Tmed5 APN 5 108,272,416 (GRCm39) missense probably benign 0.06
PIT4431001:Tmed5 UTSW 5 108,277,887 (GRCm39) missense possibly damaging 0.78
R0396:Tmed5 UTSW 5 108,273,882 (GRCm39) missense probably damaging 1.00
R2078:Tmed5 UTSW 5 108,272,471 (GRCm39) missense probably damaging 1.00
R5558:Tmed5 UTSW 5 108,272,462 (GRCm39) missense probably benign 0.00
R7173:Tmed5 UTSW 5 108,280,187 (GRCm39) missense probably benign 0.21
R7478:Tmed5 UTSW 5 108,272,495 (GRCm39) missense probably benign 0.13
R8345:Tmed5 UTSW 5 108,273,823 (GRCm39) missense probably damaging 1.00
R9563:Tmed5 UTSW 5 108,280,100 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- CTTTTCCAAGTAGGTGAGAGGCGAC -3'
(R):5'- CGAAACCGACAAGTCTGGTGTGAAG -3'

Sequencing Primer
(F):5'- TGGTAGAAACACTCCTTCCG -3'
(R):5'- TGCGAAACCCAGAAGGC -3'
Posted On 2014-03-28