Incidental Mutation 'R0164:Pcyt1a'
ID 24380
Institutional Source Beutler Lab
Gene Symbol Pcyt1a
Ensembl Gene ENSMUSG00000005615
Gene Name phosphate cytidylyltransferase 1, choline, alpha isoform
Synonyms CTalpha, Cctalpha, Cttalpha, Ctpct, CTP:phosphocholine cytidylyltransferase alpha
MMRRC Submission 038440-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0164 (G1)
Quality Score 225
Status Not validated
Chromosome 16
Chromosomal Location 32249739-32293883 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 32289004 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 282 (S282P)
Ref Sequence ENSEMBL: ENSMUSP00000110793 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000042042] [ENSMUST00000079791] [ENSMUST00000104893] [ENSMUST00000115137] [ENSMUST00000115140]
AlphaFold P49586
Predicted Effect probably benign
Transcript: ENSMUST00000042042
SMART Domains Protein: ENSMUSP00000046286
Gene: ENSMUSG00000035699

DomainStartEndE-ValueType
Pfam:Solute_trans_a 53 321 2.7e-37 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000079791
AA Change: S282P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000078721
Gene: ENSMUSG00000005615
AA Change: S282P

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: S282P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000130056
Gene: ENSMUSG00000005615
AA Change: S282P

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 benign
Transcript: ENSMUST00000115137
AA Change: V221A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000110790
Gene: ENSMUSG00000005615
AA Change: V221A

DomainStartEndE-ValueType
Pfam:CTP_transf_2 80 201 4.1e-22 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000115140
AA Change: S282P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000110793
Gene: ENSMUSG00000005615
AA Change: S282P

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
Meta Mutation Damage Score 0.3191 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.5%
Validation Efficiency 69% (18/26)
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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2010315B03Rik T C 9: 124,057,789 (GRCm39) probably benign Het
4930522L14Rik T C 5: 109,884,713 (GRCm39) K382E probably damaging Het
Adck1 A G 12: 88,422,280 (GRCm39) E297G probably damaging Het
Aldh3a2 C T 11: 61,139,714 (GRCm39) V473I probably benign Het
Arfgef3 A T 10: 18,523,663 (GRCm39) I369K possibly damaging Het
Atp1b3 T C 9: 96,220,762 (GRCm39) I178V possibly damaging Het
Axdnd1 T C 1: 156,205,956 (GRCm39) E520G possibly damaging Het
BB019430 A T 10: 58,540,093 (GRCm39) noncoding transcript Het
Btbd1 T A 7: 81,450,751 (GRCm39) Q343L probably benign Het
Catsper1 A G 19: 5,389,503 (GRCm39) T473A possibly damaging Het
Ccn4 T C 15: 66,791,059 (GRCm39) L287P probably damaging Het
Chmp6 G A 11: 119,806,349 (GRCm39) probably null Het
Cstdc7 T A 18: 42,306,608 (GRCm39) D58E probably damaging Het
D130040H23Rik T C 8: 69,755,195 (GRCm39) V200A possibly damaging Het
D830013O20Rik C T 12: 73,411,105 (GRCm39) noncoding transcript Het
Dcaf1 T A 9: 106,721,344 (GRCm39) S379T possibly damaging Het
Dhx58 T C 11: 100,586,150 (GRCm39) I624V probably benign Het
Disp3 T C 4: 148,338,708 (GRCm39) E821G probably damaging Het
Dlc1 T A 8: 37,066,594 (GRCm39) E464V probably damaging Het
Dnah10 G A 5: 124,860,898 (GRCm39) V2151I probably damaging Het
Dnah8 G A 17: 30,967,639 (GRCm39) G2617D probably benign Het
Dnah9 C A 11: 65,809,630 (GRCm39) E872* probably null Het
Dock9 T C 14: 121,835,077 (GRCm39) Y99C probably damaging Het
Dpy19l3 T A 7: 35,416,071 (GRCm39) I310F probably damaging Het
Fggy A T 4: 95,725,891 (GRCm39) I137F probably damaging Het
Gm14012 C T 2: 128,079,936 (GRCm39) noncoding transcript Het
Gm14421 A T 2: 176,748,515 (GRCm39) noncoding transcript Het
Grin2a A G 16: 9,812,685 (GRCm39) probably null Het
Incenp A G 19: 9,872,243 (GRCm39) S72P probably benign Het
Klc3 T A 7: 19,128,851 (GRCm39) N469Y possibly damaging Het
Lrrc42 A G 4: 107,104,702 (GRCm39) S88P probably benign Het
Lrrc49 G A 9: 60,587,883 (GRCm39) T93I probably benign Het
Mlycd A T 8: 120,134,380 (GRCm39) Q294L probably damaging Het
Mrpl22 T A 11: 58,062,647 (GRCm39) I19N probably benign Het
Msh3 T A 13: 92,485,717 (GRCm39) K202N probably damaging Het
Mucl2 C T 15: 103,929,445 (GRCm39) probably null Het
Ncam1 C T 9: 49,479,709 (GRCm39) D90N probably damaging Het
Nckap5 A T 1: 125,952,144 (GRCm39) D1405E possibly damaging Het
Ncoa2 A G 1: 13,256,955 (GRCm39) probably null Het
Nlrp1b A T 11: 71,054,925 (GRCm39) W844R probably damaging Het
Nmnat1 G T 4: 149,553,607 (GRCm39) N168K possibly damaging Het
Or5b96 A G 19: 12,867,809 (GRCm39) L44P probably damaging Het
Ost4 T C 5: 31,064,803 (GRCm39) H26R probably damaging Het
Otog G A 7: 45,953,655 (GRCm39) V2638M probably damaging Het
Otogl A T 10: 107,710,391 (GRCm39) I566N probably damaging Het
Prkcg G A 7: 3,377,635 (GRCm39) E581K probably damaging Het
Ralgps2 A G 1: 156,714,659 (GRCm39) probably null Het
Scmh1 T C 4: 120,387,062 (GRCm39) probably benign Het
Sgo2b T C 8: 64,391,417 (GRCm39) H150R possibly damaging Het
Sh2b3 T G 5: 121,967,100 (GRCm39) T5P probably damaging Het
Tdp2 A G 13: 25,022,222 (GRCm39) M214V probably damaging Het
Tmem204 A G 17: 25,277,324 (GRCm39) I187T probably damaging Het
Tmem208 T G 8: 106,061,326 (GRCm39) D117E probably benign Het
Tnks1bp1 C T 2: 84,889,565 (GRCm39) P631S possibly damaging Het
Tomm70a T C 16: 56,968,184 (GRCm39) V517A probably damaging Het
Ttc7 T C 17: 87,687,323 (GRCm39) V801A probably damaging Het
Txndc5 A T 13: 38,691,929 (GRCm39) C146S probably damaging Het
Ube4b G T 4: 149,444,781 (GRCm39) T493K probably damaging Het
Ufl1 A T 4: 25,256,008 (GRCm39) Y504N probably benign Het
Ulk3 T A 9: 57,497,969 (GRCm39) I90N probably damaging Het
Unc13c T C 9: 73,602,174 (GRCm39) I1357M probably benign Het
Vmn1r28 G A 6: 58,242,702 (GRCm39) A182T probably benign Het
Vmn2r91 A C 17: 18,326,399 (GRCm39) N228T probably benign Het
Zbtb6 G T 2: 37,319,600 (GRCm39) Y109* probably null Het
Zfp640 G T 13: 66,819,062 (GRCm39) noncoding transcript Het
Zfp640 C A 13: 66,819,038 (GRCm39) noncoding transcript Het
Zfp980 A G 4: 145,428,567 (GRCm39) D432G probably benign Het
Other mutations in Pcyt1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00503:Pcyt1a APN 16 32,285,919 (GRCm39) missense probably damaging 0.99
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
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
Predicted Primers
Posted On 2013-04-16