Incidental Mutation 'R5705:Pcmt1'
ID 451929
Institutional Source Beutler Lab
Gene Symbol Pcmt1
Ensembl Gene ENSMUSG00000019795
Gene Name protein-L-isoaspartate (D-aspartate) O-methyltransferase 1
Synonyms protein carboxyl methyltransferase, PIMT
MMRRC Submission 043330-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.170) question?
Stock # R5705 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 7505137-7556900 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 7513954 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Methionine at position 224 (I224M)
Ref Sequence ENSEMBL: ENSMUSP00000125144 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000159917] [ENSMUST00000161123] [ENSMUST00000162606] [ENSMUST00000163085]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000159917
AA Change: I238M

PolyPhen 2 Score 0.736 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000124932
Gene: ENSMUSG00000019795
AA Change: I238M

DomainStartEndE-ValueType
low complexity region 7 25 N/A INTRINSIC
Pfam:PCMT 66 279 1.1e-88 PFAM
Pfam:Ubie_methyltran 126 258 3.4e-7 PFAM
Pfam:Methyltransf_31 134 284 1.1e-8 PFAM
Pfam:Methyltransf_18 136 241 3e-9 PFAM
Pfam:Methyltransf_11 141 239 1.5e-6 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160250
Predicted Effect probably benign
Transcript: ENSMUST00000161123
SMART Domains Protein: ENSMUSP00000124100
Gene: ENSMUSG00000019795

DomainStartEndE-ValueType
transmembrane domain 15 37 N/A INTRINSIC
Pfam:PCMT 53 108 4.2e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000161428
SMART Domains Protein: ENSMUSP00000123758
Gene: ENSMUSG00000019795

DomainStartEndE-ValueType
Pfam:PCMT 1 160 2.7e-61 PFAM
Pfam:Ubie_methyltran 49 148 8.3e-7 PFAM
Pfam:Methyltransf_31 58 111 3.9e-8 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000162606
AA Change: I238M

PolyPhen 2 Score 0.832 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000123866
Gene: ENSMUSG00000019795
AA Change: I238M

DomainStartEndE-ValueType
low complexity region 7 25 N/A INTRINSIC
Pfam:PCMT 66 279 2e-88 PFAM
Pfam:Ubie_methyltran 126 259 1e-6 PFAM
Pfam:Methyltransf_31 134 283 3.5e-8 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000163085
AA Change: I224M

PolyPhen 2 Score 0.856 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000125144
Gene: ENSMUSG00000019795
AA Change: I224M

DomainStartEndE-ValueType
transmembrane domain 15 37 N/A INTRINSIC
Pfam:PCMT 52 265 9.1e-89 PFAM
Pfam:Ubie_methyltran 112 244 3.1e-7 PFAM
Pfam:Methyltransf_31 120 270 9.8e-9 PFAM
Pfam:Methyltransf_18 122 227 2.7e-9 PFAM
Pfam:Methyltransf_11 127 225 1.4e-6 PFAM
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
Validation Efficiency
MGI Phenotype PHENOTYPE: Homozygous disruption of this gene causes accumulation of modified proteins, growth retardation and fatal epileptic seizures. Homozygotes for one null allele also show a small spleen, altered lipid, hormone, mineral and enzyme profiles, kyphosis, enlarged brain and abnormal dendritic arborizations. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca7 T C 10: 79,851,276 (GRCm39) V2163A probably benign Het
Abcg3 G A 5: 105,116,036 (GRCm39) A266V probably damaging Het
Ago1 T C 4: 126,342,587 (GRCm39) I519V probably benign Het
Arhgap4 G A X: 72,950,423 (GRCm39) R43W probably damaging Het
Aurkb T A 11: 68,939,641 (GRCm39) L213I possibly damaging Het
Bod1l T A 5: 41,974,345 (GRCm39) Q2323L probably benign Het
Calhm5 A T 10: 33,971,989 (GRCm39) C149S probably damaging Het
Ccdc17 C T 4: 116,454,066 (GRCm39) T28I probably benign Het
Ccdc39 T C 3: 33,871,086 (GRCm39) E630G probably damaging Het
Cnih4 A G 1: 180,981,300 (GRCm39) I24V probably benign Het
Ctse C A 1: 131,592,112 (GRCm39) T146K possibly damaging Het
Ctsr A G 13: 61,309,078 (GRCm39) F226L probably damaging Het
Cyp2a22 T C 7: 26,638,640 (GRCm39) N49D probably benign Het
Defb23 C T 2: 152,301,204 (GRCm39) A123T probably benign Het
Dtx2 C A 5: 136,039,149 (GRCm39) D69E probably damaging Het
Eps8l1 T C 7: 4,473,034 (GRCm39) V91A probably benign Het
Eps8l3 C A 3: 107,798,580 (GRCm39) Q489K probably benign Het
Esyt3 A G 9: 99,200,260 (GRCm39) S645P probably benign Het
Fam161a T A 11: 22,978,869 (GRCm39) M472K unknown Het
Glp2r A G 11: 67,600,565 (GRCm39) V428A probably benign Het
Gnl1 G A 17: 36,292,492 (GRCm39) V191I probably benign Het
Hfm1 T C 5: 107,059,319 (GRCm39) I234M probably benign Het
Hlx T C 1: 184,463,062 (GRCm39) T197A probably benign Het
Hs3st2 T C 7: 120,992,305 (GRCm39) L85P probably damaging Het
Igsf9 T C 1: 172,322,338 (GRCm39) V511A possibly damaging Het
Insyn2b A G 11: 34,354,349 (GRCm39) Y473C probably damaging Het
Kcnma1 A T 14: 24,053,839 (GRCm39) C54S possibly damaging Het
Klhdc4 A G 8: 122,531,732 (GRCm39) V181A probably benign Het
Ldb3 T C 14: 34,298,986 (GRCm39) M213V probably null Het
Mertk C A 2: 128,613,321 (GRCm39) Q446K probably benign Het
Ndufs1 A G 1: 63,186,317 (GRCm39) V46A probably benign Het
Neurod4 A G 10: 130,107,271 (GRCm39) M1T probably null Het
Nlrc5 T A 8: 95,202,385 (GRCm39) C162S probably benign Het
Pald1 A G 10: 61,159,076 (GRCm39) I785T possibly damaging Het
Pisd C T 5: 32,894,707 (GRCm39) R533H probably benign Het
Plcxd3 C A 15: 4,546,676 (GRCm39) Q227K probably benign Het
Polr1b A T 2: 128,947,271 (GRCm39) K199* probably null Het
Ppp1r10 T C 17: 36,240,381 (GRCm39) V557A probably damaging Het
Ralgapa2 A G 2: 146,291,193 (GRCm39) Y248H probably damaging Het
Rsrp1 T C 4: 134,651,331 (GRCm39) S32P unknown Het
Setdb2 T G 14: 59,660,814 (GRCm39) S110R possibly damaging Het
Srcin1 A G 11: 97,439,777 (GRCm39) C152R probably benign Het
Syk A G 13: 52,765,083 (GRCm39) N70S probably benign Het
Tlr4 T A 4: 66,752,217 (GRCm39) D59E probably damaging Het
Tm9sf4 T A 2: 153,024,378 (GRCm39) I67N probably benign Het
Trim30b T A 7: 104,006,784 (GRCm39) Y24F probably damaging Het
Tsga13 A G 6: 30,876,951 (GRCm39) S189P probably damaging Het
Tspan33 A G 6: 29,717,232 (GRCm39) D210G probably benign Het
Use1 G T 8: 71,822,331 (GRCm39) R278L probably damaging Het
Wwc1 T C 11: 35,767,423 (GRCm39) N403D probably damaging Het
Zfp263 C T 16: 3,564,318 (GRCm39) P203S probably benign Het
Other mutations in Pcmt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02934:Pcmt1 APN 10 7,516,491 (GRCm39) missense probably benign 0.00
R1968:Pcmt1 UTSW 10 7,516,474 (GRCm39) nonsense probably null
R3889:Pcmt1 UTSW 10 7,524,814 (GRCm39) critical splice donor site probably null
R5454:Pcmt1 UTSW 10 7,516,509 (GRCm39) missense probably damaging 1.00
R5630:Pcmt1 UTSW 10 7,524,857 (GRCm39) missense probably damaging 1.00
R6667:Pcmt1 UTSW 10 7,538,913 (GRCm39) missense probably damaging 1.00
R7163:Pcmt1 UTSW 10 7,513,922 (GRCm39) missense probably benign 0.01
R7168:Pcmt1 UTSW 10 7,513,946 (GRCm39) missense probably damaging 1.00
R7531:Pcmt1 UTSW 10 7,556,369 (GRCm39) splice site probably null
R8012:Pcmt1 UTSW 10 7,516,527 (GRCm39) missense probably benign 0.26
R8435:Pcmt1 UTSW 10 7,515,825 (GRCm39) missense possibly damaging 0.94
R9134:Pcmt1 UTSW 10 7,520,207 (GRCm39) splice site probably benign
R9140:Pcmt1 UTSW 10 7,514,678 (GRCm39) makesense probably null
R9595:Pcmt1 UTSW 10 7,524,817 (GRCm39) missense possibly damaging 0.52
Predicted Primers PCR Primer
(F):5'- GCAGGCTAAGGTCTTAAAGCCC -3'
(R):5'- AAATGAACCCCTGAGGACGC -3'

Sequencing Primer
(F):5'- CCTTTCACCTTGACTGTGTGGAG -3'
(R):5'- CCTGAGGACGCTAAGATGTTC -3'
Posted On 2017-01-03