Incidental Mutation 'R0344:Ptdss1'
ID 26458
Institutional Source Beutler Lab
Gene Symbol Ptdss1
Ensembl Gene ENSMUSG00000021518
Gene Name phosphatidylserine synthase 1
Synonyms PtdSer Synthase-1, PSS-1
MMRRC Submission 038551-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0344 (G1)
Quality Score 225
Status Validated
Chromosome 13
Chromosomal Location 67080894-67146465 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 67081636 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 22 (R22H)
Ref Sequence ENSEMBL: ENSMUSP00000153371 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021990] [ENSMUST00000021991] [ENSMUST00000172597] [ENSMUST00000173158] [ENSMUST00000224244] [ENSMUST00000224290] [ENSMUST00000174339] [ENSMUST00000224085] [ENSMUST00000173407] [ENSMUST00000173773] [ENSMUST00000173910]
AlphaFold Q99LH2
Predicted Effect probably benign
Transcript: ENSMUST00000021990
AA Change: R22H

PolyPhen 2 Score 0.420 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000021990
Gene: ENSMUSG00000021518
AA Change: R22H

DomainStartEndE-ValueType
transmembrane domain 37 59 N/A INTRINSIC
transmembrane domain 72 89 N/A INTRINSIC
Pfam:PSS 96 372 1.3e-108 PFAM
transmembrane domain 383 405 N/A INTRINSIC
low complexity region 442 464 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000021991
SMART Domains Protein: ENSMUSP00000021991
Gene: ENSMUSG00000021519

DomainStartEndE-ValueType
low complexity region 97 117 N/A INTRINSIC
Mterf 161 196 1.63e3 SMART
Mterf 201 231 7.37e-1 SMART
Mterf 236 267 4.68e-3 SMART
Mterf 272 303 2.12e-1 SMART
Mterf 308 339 4.11e1 SMART
Mterf 340 370 9.22e-2 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000172597
SMART Domains Protein: ENSMUSP00000133433
Gene: ENSMUSG00000021519

DomainStartEndE-ValueType
low complexity region 97 117 N/A INTRINSIC
PDB:3OPG|A 121 204 2e-40 PDB
Blast:Mterf 161 196 1e-15 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172807
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173062
Predicted Effect probably benign
Transcript: ENSMUST00000173158
SMART Domains Protein: ENSMUSP00000134032
Gene: ENSMUSG00000021519

DomainStartEndE-ValueType
low complexity region 97 108 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174011
Predicted Effect possibly damaging
Transcript: ENSMUST00000224244
AA Change: R22H

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)
Predicted Effect probably damaging
Transcript: ENSMUST00000224290
AA Change: R22H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect probably benign
Transcript: ENSMUST00000174339
SMART Domains Protein: ENSMUSP00000134286
Gene: ENSMUSG00000021519

DomainStartEndE-ValueType
low complexity region 97 117 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000224085
Predicted Effect probably benign
Transcript: ENSMUST00000173407
SMART Domains Protein: ENSMUSP00000133594
Gene: ENSMUSG00000021519

DomainStartEndE-ValueType
low complexity region 97 108 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000173773
Predicted Effect probably benign
Transcript: ENSMUST00000173910
SMART Domains Protein: ENSMUSP00000133456
Gene: ENSMUSG00000021519

DomainStartEndE-ValueType
low complexity region 23 41 N/A INTRINSIC
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.2%
  • 10x: 96.3%
  • 20x: 93.6%
Validation Efficiency 99% (81/82)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene catalyzes the formation of phosphatidylserine from either phosphatidylcholine or phosphatidylethanolamine. Phosphatidylserine localizes to the mitochondria-associated membrane of the endoplasmic reticulum, where it serves a structural role as well as a signaling role. Defects in this gene are a cause of Lenz-Majewski hyperostotic dwarfism. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2014]
PHENOTYPE: Mice homozygous for a null allele exhibit decreased phosphatidylethanolamine and phosphatidylserine levels in the liver but normal axon growth and life span. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930553J12Rik T A 16: 88,617,189 (GRCm39) C29* probably null Het
Abca4 G A 3: 121,877,613 (GRCm39) C324Y probably damaging Het
Ablim2 T G 5: 35,994,277 (GRCm39) probably benign Het
Abr A T 11: 76,369,870 (GRCm39) V115E probably damaging Het
Adgrl2 C T 3: 148,571,231 (GRCm39) probably null Het
Aff3 A T 1: 38,243,013 (GRCm39) S936T probably benign Het
Agap3 T C 5: 24,656,200 (GRCm39) probably benign Het
Ahrr T A 13: 74,362,705 (GRCm39) S393C probably damaging Het
Amfr T C 8: 94,713,998 (GRCm39) probably null Het
Ankrd26 C A 6: 118,484,598 (GRCm39) probably null Het
Asxl3 G A 18: 22,650,668 (GRCm39) V886I probably benign Het
Atp5f1a C A 18: 77,867,895 (GRCm39) N356K probably damaging Het
AU021092 A T 16: 5,040,031 (GRCm39) M31K possibly damaging Het
Bicral A G 17: 47,124,978 (GRCm39) probably benign Het
Btbd9 C T 17: 30,493,916 (GRCm39) D492N possibly damaging Het
C3ar1 T C 6: 122,827,731 (GRCm39) D162G probably benign Het
Camkk2 C T 5: 122,901,940 (GRCm39) C123Y probably benign Het
Casp8ap2 A T 4: 32,644,079 (GRCm39) I1051F probably damaging Het
Catsperg1 A T 7: 28,894,965 (GRCm39) V544E probably damaging Het
Cdc27 G A 11: 104,417,817 (GRCm39) probably benign Het
Colec12 C T 18: 9,858,921 (GRCm39) P568L unknown Het
Dennd6b T C 15: 89,080,432 (GRCm39) Q56R probably benign Het
Dmac2l T C 12: 69,787,663 (GRCm39) probably benign Het
Fbxl17 G A 17: 63,692,062 (GRCm39) probably benign Het
Fubp1 T C 3: 151,925,350 (GRCm39) V164A probably damaging Het
Gdap2 G A 3: 100,085,572 (GRCm39) G165S probably damaging Het
Gns A G 10: 121,219,328 (GRCm39) K352E probably benign Het
Gtf2ird2 C T 5: 134,220,088 (GRCm39) T22M probably damaging Het
Herc3 A G 6: 58,845,613 (GRCm39) probably benign Het
Hp1bp3 C T 4: 137,964,520 (GRCm39) S348F probably damaging Het
Inpp1 A T 1: 52,838,513 (GRCm39) F45L probably damaging Het
Ipo4 T C 14: 55,863,399 (GRCm39) Q1073R possibly damaging Het
Itgae A G 11: 73,008,973 (GRCm39) K485E probably benign Het
Jak2 G A 19: 29,261,029 (GRCm39) V342I probably damaging Het
Kptn C A 7: 15,859,666 (GRCm39) Q297K probably damaging Het
Lims2 A G 18: 32,077,573 (GRCm39) E103G probably benign Het
Mthfr C G 4: 148,139,885 (GRCm39) S618W probably damaging Het
Nanos3 C T 8: 84,902,763 (GRCm39) R133Q probably damaging Het
Nup133 A G 8: 124,644,185 (GRCm39) V727A possibly damaging Het
Oas2 T G 5: 120,881,152 (GRCm39) E313A probably damaging Het
Or10d4c G A 9: 39,558,646 (GRCm39) C208Y probably damaging Het
Or52b2 C A 7: 104,986,814 (GRCm39) M36I probably benign Het
Or5b105 G A 19: 13,080,642 (GRCm39) R3C possibly damaging Het
Or5m8 T A 2: 85,822,726 (GRCm39) C188* probably null Het
Or5p63 A T 7: 107,810,949 (GRCm39) Y262* probably null Het
Park7 A G 4: 150,992,806 (GRCm39) V20A possibly damaging Het
Pgap4 T C 4: 49,586,566 (GRCm39) T201A probably benign Het
Phldb1 C A 9: 44,612,964 (GRCm39) V919L probably benign Het
Pkhd1l1 C A 15: 44,460,407 (GRCm39) H4205Q probably benign Het
Plekhg3 G T 12: 76,613,040 (GRCm39) E449* probably null Het
Pramel26 A T 4: 143,537,338 (GRCm39) I331N probably damaging Het
Pstpip1 T C 9: 56,033,929 (GRCm39) V301A probably benign Het
Ptprq A G 10: 107,541,443 (GRCm39) V361A probably benign Het
Ralgapa2 A T 2: 146,188,714 (GRCm39) V1309E possibly damaging Het
Rere T C 4: 150,695,438 (GRCm39) probably benign Het
Sbk3 T A 7: 4,970,404 (GRCm39) T322S possibly damaging Het
Scn9a T A 2: 66,335,354 (GRCm39) I1203L probably damaging Het
Setdb1 A T 3: 95,233,442 (GRCm39) probably benign Het
Sik3 C A 9: 46,120,109 (GRCm39) Q683K probably damaging Het
Slc24a5 A G 2: 124,927,621 (GRCm39) I307V probably benign Het
Smg6 A G 11: 74,820,647 (GRCm39) D306G probably damaging Het
Snx13 G A 12: 35,136,899 (GRCm39) W120* probably null Het
Snx5 A G 2: 144,099,128 (GRCm39) probably benign Het
Srsf5 T C 12: 80,994,298 (GRCm39) S76P probably benign Het
Stard6 A G 18: 70,629,186 (GRCm39) D31G probably damaging Het
Taf3 A G 2: 9,956,709 (GRCm39) M333T probably benign Het
Taf6 T G 5: 138,179,409 (GRCm39) I377L probably benign Het
Taf8 G T 17: 47,804,505 (GRCm39) N252K probably benign Het
Tfap2c A G 2: 172,393,423 (GRCm39) T113A probably benign Het
Tmtc4 C T 14: 123,215,572 (GRCm39) V25M probably damaging Het
Topbp1 T A 9: 103,205,886 (GRCm39) D841E probably damaging Het
Topbp1 T A 9: 103,185,932 (GRCm39) probably benign Het
Ttn A T 2: 76,542,833 (GRCm39) D33384E probably damaging Het
Unc13c T C 9: 73,838,067 (GRCm39) E928G probably benign Het
Vav1 T C 17: 57,603,090 (GRCm39) F81L probably damaging Het
Vmn2r63 A G 7: 42,553,042 (GRCm39) I738T probably damaging Het
Vmn2r87 C T 10: 130,315,806 (GRCm39) E87K probably damaging Het
Zfp229 A T 17: 21,964,822 (GRCm39) M351L probably benign Het
Other mutations in Ptdss1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01825:Ptdss1 APN 13 67,135,886 (GRCm39) missense probably benign 0.02
IGL02798:Ptdss1 APN 13 67,124,824 (GRCm39) missense probably damaging 1.00
IGL03114:Ptdss1 APN 13 67,142,058 (GRCm39) nonsense probably null
BB009:Ptdss1 UTSW 13 67,114,496 (GRCm39) missense probably damaging 1.00
BB019:Ptdss1 UTSW 13 67,114,496 (GRCm39) missense probably damaging 1.00
R0591:Ptdss1 UTSW 13 67,120,714 (GRCm39) splice site probably benign
R0749:Ptdss1 UTSW 13 67,135,914 (GRCm39) nonsense probably null
R0759:Ptdss1 UTSW 13 67,135,868 (GRCm39) missense probably damaging 1.00
R1140:Ptdss1 UTSW 13 67,111,420 (GRCm39) missense probably benign 0.00
R1500:Ptdss1 UTSW 13 67,143,472 (GRCm39) missense probably benign 0.04
R1676:Ptdss1 UTSW 13 67,081,701 (GRCm39) missense probably damaging 1.00
R1761:Ptdss1 UTSW 13 67,104,476 (GRCm39) missense possibly damaging 0.72
R2086:Ptdss1 UTSW 13 67,101,619 (GRCm39) missense probably benign 0.00
R2087:Ptdss1 UTSW 13 67,124,881 (GRCm39) splice site probably benign
R3962:Ptdss1 UTSW 13 67,142,075 (GRCm39) missense probably benign 0.00
R4662:Ptdss1 UTSW 13 67,081,675 (GRCm39) missense possibly damaging 0.95
R4707:Ptdss1 UTSW 13 67,143,482 (GRCm39) critical splice donor site probably null
R4775:Ptdss1 UTSW 13 67,135,922 (GRCm39) splice site probably null
R4993:Ptdss1 UTSW 13 67,093,352 (GRCm39) missense probably benign 0.01
R5402:Ptdss1 UTSW 13 67,081,663 (GRCm39) missense possibly damaging 0.88
R5463:Ptdss1 UTSW 13 67,093,365 (GRCm39) missense probably damaging 1.00
R5643:Ptdss1 UTSW 13 67,120,604 (GRCm39) missense probably damaging 1.00
R5644:Ptdss1 UTSW 13 67,120,604 (GRCm39) missense probably damaging 1.00
R6043:Ptdss1 UTSW 13 67,111,433 (GRCm39) missense probably damaging 1.00
R6145:Ptdss1 UTSW 13 67,120,701 (GRCm39) critical splice donor site probably null
R6726:Ptdss1 UTSW 13 67,101,595 (GRCm39) nonsense probably null
R7016:Ptdss1 UTSW 13 67,120,685 (GRCm39) missense probably benign 0.00
R7116:Ptdss1 UTSW 13 67,093,391 (GRCm39) missense probably benign 0.00
R7339:Ptdss1 UTSW 13 67,111,426 (GRCm39) missense possibly damaging 0.78
R7836:Ptdss1 UTSW 13 67,081,719 (GRCm39) missense probably benign
R7932:Ptdss1 UTSW 13 67,114,496 (GRCm39) missense probably damaging 1.00
R7939:Ptdss1 UTSW 13 67,143,411 (GRCm39) missense probably benign
R8015:Ptdss1 UTSW 13 67,111,407 (GRCm39) missense possibly damaging 0.87
R8237:Ptdss1 UTSW 13 67,124,841 (GRCm39) missense probably damaging 1.00
R8767:Ptdss1 UTSW 13 67,101,608 (GRCm39) missense probably benign 0.01
RF044:Ptdss1 UTSW 13 67,093,412 (GRCm39) missense possibly damaging 0.47
Predicted Primers PCR Primer
(F):5'- TACTAGGCTGCTTCTTCAGGCTGC -3'
(R):5'- AGCTAGGTGACCTGCATGAGTTCC -3'

Sequencing Primer
(F):5'- CTTCTCAGGGTGCCAGAC -3'
(R):5'- CGTGGAACAGCTACTCACTTC -3'
Posted On 2013-04-16