Incidental Mutation 'IGL00503:Pcyt1a'
ID 332488
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Pcyt1a
Ensembl Gene ENSMUSG00000005615
Gene Name phosphate cytidylyltransferase 1, choline, alpha isoform
Synonyms CTalpha, Cctalpha, Cttalpha, Ctpct, CTP:phosphocholine cytidylyltransferase alpha
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL00503
Quality Score
Status
Chromosome 16
Chromosomal Location 32249739-32293883 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 32285919 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 197 (T197A)
Ref Sequence ENSEMBL: ENSMUSP00000110793 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000079791] [ENSMUST00000104893] [ENSMUST00000115137] [ENSMUST00000115140]
AlphaFold P49586
Predicted Effect probably damaging
Transcript: ENSMUST00000079791
AA Change: T197A

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000078721
Gene: ENSMUSG00000005615
AA Change: T197A

DomainStartEndE-ValueType
Pfam:CTP_transf_2 80 208 6.4e-24 PFAM
low complexity region 244 262 N/A INTRINSIC
low complexity region 328 352 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000104893
AA Change: T197A

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000130056
Gene: ENSMUSG00000005615
AA Change: T197A

DomainStartEndE-ValueType
Pfam:CTP_transf_2 80 208 6.4e-24 PFAM
low complexity region 244 262 N/A INTRINSIC
low complexity region 328 352 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000115137
AA Change: T197A

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000110790
Gene: ENSMUSG00000005615
AA Change: T197A

DomainStartEndE-ValueType
Pfam:CTP_transf_2 80 201 4.1e-22 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000115140
AA Change: T197A

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000110793
Gene: ENSMUSG00000005615
AA Change: T197A

DomainStartEndE-ValueType
Pfam:CTP_transf_like 80 208 3.2e-33 PFAM
low complexity region 244 262 N/A INTRINSIC
low complexity region 328 352 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231920
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the cytidylyltransferase family and is involved in the regulation of phosphatidylcholine biosynthesis. Mutations in this gene are associated with spondylometaphyseal dysplasia with cone-rod dystrophy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]
PHENOTYPE: Embryos homozygous for a targeted null mutation fail to form blastocysts, do not develop past E3.5, and fail to implant. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930546C10Rik T A 18: 69,083,173 (GRCm39) R14* probably null Het
Abcb5 A G 12: 118,871,336 (GRCm39) S688P probably benign Het
Adgb T A 10: 10,281,843 (GRCm39) Q597L possibly damaging Het
Aga G A 8: 53,971,956 (GRCm39) V210I probably benign Het
Akap17b A G X: 35,875,963 (GRCm39) S515P probably damaging Het
Brinp3 A T 1: 146,776,905 (GRCm39) T451S probably benign Het
Cabcoco1 G T 10: 68,377,635 (GRCm39) T18N possibly damaging Het
Ccar2 C T 14: 70,379,980 (GRCm39) W402* probably null Het
Ccdc15 G A 9: 37,231,769 (GRCm39) A185V probably damaging Het
Ccdc50 G A 16: 27,228,102 (GRCm39) E90K probably damaging Het
Cckbr G A 7: 105,083,449 (GRCm39) M217I probably benign Het
Clec16a A G 16: 10,512,513 (GRCm39) T398A possibly damaging Het
Col4a1 A G 8: 11,290,076 (GRCm39) probably benign Het
Cyp4v3 T A 8: 45,760,058 (GRCm39) E498V probably damaging Het
Dgke T C 11: 88,932,327 (GRCm39) I488V probably benign Het
Dip2c A G 13: 9,617,934 (GRCm39) D443G probably damaging Het
Edem3 T G 1: 151,694,264 (GRCm39) S852A probably benign Het
Fbxo8 T A 8: 57,041,058 (GRCm39) M158K probably benign Het
Galnt15 C T 14: 31,774,313 (GRCm39) T359M possibly damaging Het
Herc6 A G 6: 57,584,130 (GRCm39) N330D probably benign Het
Kdf1 T C 4: 133,255,468 (GRCm39) S62P probably damaging Het
Larp4 T A 15: 99,885,302 (GRCm39) I51N probably damaging Het
Mfsd6l T A 11: 68,447,299 (GRCm39) I50N probably damaging Het
Mroh2b A G 15: 4,928,679 (GRCm39) Y4C probably benign Het
Muc17 G T 5: 137,165,971 (GRCm39) Y343* probably null Het
Myom2 A C 8: 15,164,289 (GRCm39) probably null Het
Npat A T 9: 53,483,949 (GRCm39) probably benign Het
Pamr1 A T 2: 102,472,617 (GRCm39) I639F possibly damaging Het
Pcsk2 A G 2: 143,635,159 (GRCm39) S345G probably damaging Het
Pkd1 A G 17: 24,784,401 (GRCm39) M316V probably benign Het
Plekhs1 T C 19: 56,453,031 (GRCm39) probably null Het
Sema3e G T 5: 14,290,586 (GRCm39) R557M probably damaging Het
Sgsm1 T C 5: 113,424,008 (GRCm39) N154S probably benign Het
Smg1 A T 7: 117,784,706 (GRCm39) probably benign Het
Sp110 A C 1: 85,505,050 (GRCm39) F434C probably benign Het
Spats1 A T 17: 45,765,011 (GRCm39) probably null Het
Tnfaip6 T G 2: 51,945,859 (GRCm39) V235G probably damaging Het
Trim34a A T 7: 103,910,538 (GRCm39) T447S probably damaging Het
Tut1 G A 19: 8,936,460 (GRCm39) A95T probably damaging Het
Urgcp C T 11: 5,666,448 (GRCm39) R630Q possibly damaging Het
Vmn1r125 G T 7: 21,006,106 (GRCm39) M1I probably null Het
Vmn2r99 A G 17: 19,599,116 (GRCm39) T267A probably benign Het
Wdr5 A G 2: 27,410,879 (GRCm39) K162E probably benign Het
Zscan26 T G 13: 21,629,271 (GRCm39) K285Q probably damaging Het
Other mutations in Pcyt1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02147:Pcyt1a APN 16 32,280,916 (GRCm39) missense probably damaging 1.00
willingly UTSW 16 32,285,899 (GRCm39) missense probably damaging 0.98
R0164:Pcyt1a UTSW 16 32,289,004 (GRCm39) missense probably damaging 1.00
R0164:Pcyt1a UTSW 16 32,289,004 (GRCm39) missense probably damaging 1.00
R1529:Pcyt1a UTSW 16 32,270,611 (GRCm39) missense possibly damaging 0.45
R1607:Pcyt1a UTSW 16 32,285,937 (GRCm39) missense probably damaging 0.96
R4693:Pcyt1a UTSW 16 32,289,042 (GRCm39) unclassified probably benign
R4998:Pcyt1a UTSW 16 32,270,660 (GRCm39) splice site probably benign
R6488:Pcyt1a UTSW 16 32,285,899 (GRCm39) missense probably damaging 0.98
R6852:Pcyt1a UTSW 16 32,288,938 (GRCm39) missense probably damaging 0.99
R9091:Pcyt1a UTSW 16 32,285,332 (GRCm39) missense probably benign
R9254:Pcyt1a UTSW 16 32,288,894 (GRCm39) missense probably benign 0.00
R9270:Pcyt1a UTSW 16 32,285,332 (GRCm39) missense probably benign
Z1177:Pcyt1a UTSW 16 32,290,278 (GRCm39) missense probably benign
Posted On 2015-08-05