Incidental Mutation 'R2425:Pdxdc1'
ID250172
Institutional Source Beutler Lab
Gene Symbol Pdxdc1
Ensembl Gene ENSMUSG00000022680
Gene Namepyridoxal-dependent decarboxylase domain containing 1
Synonyms2210010A19Rik
MMRRC Submission 040387-MU
Accession Numbers
Is this an essential gene? Probably non essential (E-score: 0.144) question?
Stock #R2425 (G1)
Quality Score225
Status Not validated
Chromosome16
Chromosomal Location13833148-13903131 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 13879508 bp
ZygosityHeterozygous
Amino Acid Change Serine to Threonine at position 103 (S103T)
Ref Sequence ENSEMBL: ENSMUSP00000111471 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023361] [ENSMUST00000115802] [ENSMUST00000115803] [ENSMUST00000115804]
Predicted Effect possibly damaging
Transcript: ENSMUST00000023361
AA Change: S103T

PolyPhen 2 Score 0.825 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680
AA Change: S103T

DomainStartEndE-ValueType
Pfam:Pyridoxal_deC 166 310 2.6e-12 PFAM
coiled coil region 610 631 N/A INTRINSIC
low complexity region 683 695 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000115802
AA Change: S103T

PolyPhen 2 Score 0.887 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000111468
Gene: ENSMUSG00000022680
AA Change: S103T

DomainStartEndE-ValueType
Pfam:Pyridoxal_deC 153 316 1.8e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000115803
AA Change: S103T

PolyPhen 2 Score 0.126 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000111469
Gene: ENSMUSG00000022680
AA Change: S103T

DomainStartEndE-ValueType
Pfam:Pyridoxal_deC 190 293 1.4e-13 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000115804
AA Change: S103T

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680
AA Change: S103T

DomainStartEndE-ValueType
Pfam:Pyridoxal_deC 154 308 5.5e-15 PFAM
coiled coil region 610 631 N/A INTRINSIC
low complexity region 683 695 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139859
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148551
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151774
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154150
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 93.5%
Validation Efficiency
MGI Phenotype Homozygous mutant mice exhibit behavioral and learning defects including abnormal spontaneous activity, impaired spatial memory, and reduced exploratory activity in the presence of conspecifics.,NO_PHENOTYPE
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca15 T C 7: 120,359,810 F621S probably damaging Het
Abcc10 A G 17: 46,310,157 Y976H probably damaging Het
Abhd6 T A 14: 8,049,857 N215K probably benign Het
Adcy4 T C 14: 55,778,017 T479A probably damaging Het
Amacr A G 15: 10,983,368 Q88R possibly damaging Het
Ankrd11 T A 8: 122,893,163 I1317F possibly damaging Het
Ano3 C A 2: 110,862,843 A137S probably benign Het
Astn1 T G 1: 158,579,666 S562A probably damaging Het
Cd44 T A 2: 102,861,586 Y119F probably damaging Het
CN725425 A C 15: 91,245,855 D307A probably damaging Het
Col12a1 T C 9: 79,678,366 Y1243C probably damaging Het
Cyp2c50 T C 19: 40,089,848 I50T probably benign Het
Dhrs9 A G 2: 69,392,964 K19E probably benign Het
Dnajb14 T G 3: 137,892,905 F135V probably null Het
Draxin T A 4: 148,112,756 T195S possibly damaging Het
Elane C T 10: 79,887,776 R192C probably benign Het
Fam171a2 A C 11: 102,438,361 I524S possibly damaging Het
Fam35a A G 14: 34,268,689 S87P probably damaging Het
Fbxo10 C T 4: 45,051,642 E490K possibly damaging Het
Fkbp15 T C 4: 62,312,365 T704A probably benign Het
Fndc1 T A 17: 7,805,018 D35V probably damaging Het
Galntl5 A G 5: 25,220,081 K366E probably damaging Het
Gas7 G A 11: 67,643,295 A74T probably benign Het
Gjd4 G T 18: 9,280,811 S89* probably null Het
Gldc T A 19: 30,131,790 N583Y probably damaging Het
Gpr161 T A 1: 165,310,623 S259R possibly damaging Het
Igfn1 T A 1: 135,963,102 T2387S probably damaging Het
Il3 A T 11: 54,265,549 V119D possibly damaging Het
Ints3 T C 3: 90,394,110 T822A possibly damaging Het
Jakmip1 C T 5: 37,141,805 Q790* probably null Het
Kcne1 A G 16: 92,348,758 I66T probably damaging Het
Nipbl A G 15: 8,351,482 S609P probably benign Het
Olfr1053 A G 2: 86,314,395 V297A probably damaging Het
Olfr330 A G 11: 58,529,311 I225T probably damaging Het
Olfr975 T C 9: 39,949,841 E310G probably null Het
Pla2g2a C A 4: 138,832,918 A24E possibly damaging Het
Plxna2 C T 1: 194,749,317 S538F probably damaging Het
Pramel1 T G 4: 143,398,466 L320R probably damaging Het
Rad23b T A 4: 55,385,438 I325N probably damaging Het
Rasgrp1 C G 2: 117,289,450 probably null Het
Rbm12b1 T A 4: 12,146,443 I805N probably damaging Het
Slc12a9 G T 5: 137,315,597 A700E probably damaging Het
Tbc1d24 A T 17: 24,186,008 V54E probably damaging Het
Tmc8 A G 11: 117,792,569 D650G probably damaging Het
Upf1 C T 8: 70,338,460 R544H probably damaging Het
Ush2a T A 1: 188,537,804 N1749K possibly damaging Het
Usp42 T C 5: 143,715,839 T810A probably benign Het
Wdr70 C A 15: 7,887,359 E526* probably null Het
Zfp935 G T 13: 62,455,108 Q93K probably benign Het
Other mutations in Pdxdc1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01760:Pdxdc1 APN 16 13859152 missense probably damaging 1.00
IGL02101:Pdxdc1 APN 16 13869856 missense probably damaging 0.99
IGL02484:Pdxdc1 APN 16 13876081 missense possibly damaging 0.94
IGL02523:Pdxdc1 APN 16 13881935 missense probably damaging 1.00
IGL02560:Pdxdc1 APN 16 13839732 missense probably benign 0.00
IGL02884:Pdxdc1 APN 16 13843795 missense possibly damaging 0.86
IGL03008:Pdxdc1 APN 16 13876159 missense possibly damaging 0.81
IGL03162:Pdxdc1 APN 16 13857417 missense probably damaging 0.99
IGL02991:Pdxdc1 UTSW 16 13857396 missense probably damaging 1.00
PIT4472001:Pdxdc1 UTSW 16 13845345 missense probably damaging 1.00
R0015:Pdxdc1 UTSW 16 13887683 splice site probably benign
R0240:Pdxdc1 UTSW 16 13879445 missense probably damaging 1.00
R0240:Pdxdc1 UTSW 16 13879445 missense probably damaging 1.00
R0432:Pdxdc1 UTSW 16 13854400 missense probably damaging 0.97
R0846:Pdxdc1 UTSW 16 13854393 critical splice donor site probably null
R0944:Pdxdc1 UTSW 16 13838369 missense probably damaging 1.00
R0945:Pdxdc1 UTSW 16 13857432 missense probably damaging 1.00
R1118:Pdxdc1 UTSW 16 13879414 splice site probably benign
R1726:Pdxdc1 UTSW 16 13838300 critical splice donor site probably null
R3890:Pdxdc1 UTSW 16 13836448 missense probably benign
R4452:Pdxdc1 UTSW 16 13837126 missense possibly damaging 0.55
R4516:Pdxdc1 UTSW 16 13838346 nonsense probably null
R4938:Pdxdc1 UTSW 16 13876069 missense probably benign 0.03
R5352:Pdxdc1 UTSW 16 13840311 missense probably benign 0.01
R5554:Pdxdc1 UTSW 16 13872499 missense probably benign 0.01
R7300:Pdxdc1 UTSW 16 13879510 missense probably damaging 0.99
R7356:Pdxdc1 UTSW 16 13860003 missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACATTGCCCATAATATCTTTACCATT -3'
(R):5'- TTCTCCCCACACTTTGAGCA -3'

Sequencing Primer
(F):5'- AATCCGGCGTAGCCATAA -3'
(R):5'- CACACTTTGAGCATCTTGAGGAC -3'
Posted On2014-11-12