Incidental Mutation 'R7659:Ppt1'
ID 591422
Institutional Source Beutler Lab
Gene Symbol Ppt1
Ensembl Gene ENSMUSG00000028657
Gene Name palmitoyl-protein thioesterase 1
Synonyms CLN1, 9530043G02Rik, D4Ertd184e
MMRRC Submission 045734-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7659 (G1)
Quality Score 225.009
Status Validated
Chromosome 4
Chromosomal Location 122730035-122752968 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 122730126 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Glutamine at position 26 (H26Q)
Ref Sequence ENSEMBL: ENSMUSP00000030412 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030412] [ENSMUST00000097902] [ENSMUST00000120157] [ENSMUST00000121870]
AlphaFold O88531
Predicted Effect probably benign
Transcript: ENSMUST00000030412
AA Change: H26Q

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000030412
Gene: ENSMUSG00000028657
AA Change: H26Q

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Pfam:Palm_thioest 28 306 3.6e-208 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000097902
AA Change: H26Q

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000095512
Gene: ENSMUSG00000028657
AA Change: H26Q

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Pfam:Palm_thioest 28 188 4e-110 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000120157
AA Change: H26Q
SMART Domains Protein: ENSMUSP00000113258
Gene: ENSMUSG00000028657
AA Change: H26Q

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000121870
AA Change: H26Q

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000113367
Gene: ENSMUSG00000028657
AA Change: H26Q

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Pfam:Palm_thioest 28 179 6e-108 PFAM
Meta Mutation Damage Score 0.1991 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency 100% (66/66)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a small glycoprotein involved in the catabolism of lipid-modified proteins during lysosomal degradation. The encoded enzyme removes thioester-linked fatty acyl groups such as palmitate from cysteine residues. Defects in this gene are a cause of infantile neuronal ceroid lipofuscinosis 1 (CLN1, or INCL) and neuronal ceroid lipofuscinosis 4 (CLN4). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit neuronal loss associated with accumulation of autofluorescent storage material in brain, late-onset progressive motor defects, seizures, and death by 10 months of age. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aldh2 T C 5: 121,707,023 (GRCm39) E498G probably damaging Het
Ankar T C 1: 72,729,294 (GRCm39) T284A possibly damaging Het
Arid5b C T 10: 67,934,417 (GRCm39) G495E probably benign Het
Armh1 C A 4: 117,070,938 (GRCm39) A396S probably benign Het
Atp6v0a4 A G 6: 38,048,907 (GRCm39) I452T probably damaging Het
Azgp1 G T 5: 137,985,775 (GRCm39) A133S probably damaging Het
Bmp2k T C 5: 97,222,578 (GRCm39) S667P unknown Het
C1qtnf9 T A 14: 61,009,753 (GRCm39) I3N possibly damaging Het
C530025M09Rik T G 2: 149,672,539 (GRCm39) T199P unknown Het
Casc3 C G 11: 98,700,699 (GRCm39) R4G unknown Het
Cass4 A G 2: 172,268,947 (GRCm39) D343G probably damaging Het
Cenatac T C 9: 44,324,790 (GRCm39) E164G probably damaging Het
Col6a3 T A 1: 90,709,467 (GRCm39) T2517S unknown Het
Dbr1 A G 9: 99,458,663 (GRCm39) T78A probably damaging Het
Dnah9 A G 11: 65,880,606 (GRCm39) F2664L probably damaging Het
Eif2ak1 T C 5: 143,826,280 (GRCm39) I431T probably damaging Het
Got1 A G 19: 43,493,078 (GRCm39) V281A probably benign Het
Gpld1 A C 13: 25,163,964 (GRCm39) R555S probably benign Het
Gpr149 T C 3: 62,511,256 (GRCm39) R248G probably benign Het
Hps3 G A 3: 20,076,978 (GRCm39) R395* probably null Het
Inpp5b T C 4: 124,689,219 (GRCm39) L833P probably damaging Het
Itgb4 A T 11: 115,870,557 (GRCm39) S129C probably damaging Het
Kif1a T A 1: 92,974,542 (GRCm39) probably benign Het
Lgr4 T A 2: 109,827,111 (GRCm39) V205E probably damaging Het
Mbd3 T C 10: 80,231,019 (GRCm39) N96S probably damaging Het
Mcam T A 9: 44,048,067 (GRCm39) C136S unknown Het
Mki67 A G 7: 135,299,155 (GRCm39) S1960P probably damaging Het
Mogs G A 6: 83,093,806 (GRCm39) probably null Het
Muc6 T C 7: 141,216,973 (GRCm39) T2567A possibly damaging Het
Mug1 C A 6: 121,838,179 (GRCm39) H470N possibly damaging Het
Nae1 A G 8: 105,242,796 (GRCm39) V432A probably benign Het
Nav3 T G 10: 109,602,851 (GRCm39) T1233P probably benign Het
Nme9 G A 9: 99,352,910 (GRCm39) A287T possibly damaging Het
Nmrk1 A G 19: 18,613,499 (GRCm39) I8V probably benign Het
Noa1 T C 5: 77,457,237 (GRCm39) N223D not run Het
Nr4a3 T C 4: 48,051,269 (GRCm39) Y8H probably damaging Het
Or12e1 T A 2: 87,022,709 (GRCm39) V226E possibly damaging Het
Or1j15 T A 2: 36,458,637 (GRCm39) V9E possibly damaging Het
Or2b4 A T 17: 38,116,054 (GRCm39) Q6L probably benign Het
Or4n4b T C 14: 50,536,698 (GRCm39) I23V probably benign Het
Or4p20 T C 2: 88,254,270 (GRCm39) Y33C probably damaging Het
Or52h2 T C 7: 103,839,394 (GRCm39) S7G probably benign Het
Or7g29 C T 9: 19,286,854 (GRCm39) A108T probably benign Het
Or8c9 T C 9: 38,241,012 (GRCm39) V40A possibly damaging Het
Otoa T A 7: 120,733,267 (GRCm39) H711Q probably benign Het
Otogl T A 10: 107,612,981 (GRCm39) E2048D probably benign Het
Paip1 C T 13: 119,587,306 (GRCm39) T390I possibly damaging Het
Pcdha3 A G 18: 37,081,219 (GRCm39) T654A probably benign Het
Pigg G A 5: 108,486,485 (GRCm39) V713I probably benign Het
Prim1 T C 10: 127,862,458 (GRCm39) probably null Het
Prmt7 G T 8: 106,963,918 (GRCm39) A271S probably benign Het
Ptprd T C 4: 76,047,153 (GRCm39) D124G probably benign Het
Rad54l2 T C 9: 106,590,777 (GRCm39) K450E probably benign Het
Rasgrp2 G T 19: 6,451,857 (GRCm39) V13L probably damaging Het
Sapcd2 A G 2: 25,265,978 (GRCm39) probably null Het
Siglecf A G 7: 43,001,194 (GRCm39) Y54C probably damaging Het
Stk31 T A 6: 49,400,340 (GRCm39) N388K probably benign Het
Timm23 A C 14: 31,920,935 (GRCm39) Y52* probably null Het
Tm9sf1 A T 14: 55,873,792 (GRCm39) F569I probably damaging Het
Tmprss9 C A 10: 80,728,843 (GRCm39) A592E probably damaging Het
Trim30d A T 7: 104,121,554 (GRCm39) V397E probably benign Het
Tshz1 A T 18: 84,034,200 (GRCm39) N69K probably damaging Het
Upk2 A C 9: 44,364,808 (GRCm39) S130R probably damaging Het
Vmn1r80 A G 7: 11,926,977 (GRCm39) Y29C probably damaging Het
Vmn2r96 T C 17: 18,793,749 (GRCm39) I31T probably benign Het
Zfp975 T C 7: 42,311,848 (GRCm39) Q255R probably benign Het
Other mutations in Ppt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01068:Ppt1 APN 4 122,737,800 (GRCm39) missense probably damaging 1.00
IGL01346:Ppt1 APN 4 122,737,848 (GRCm39) missense probably damaging 0.98
IGL01511:Ppt1 APN 4 122,748,218 (GRCm39) missense probably damaging 0.99
IGL01719:Ppt1 APN 4 122,737,860 (GRCm39) missense probably damaging 1.00
R0008:Ppt1 UTSW 4 122,742,216 (GRCm39) splice site probably benign
R0008:Ppt1 UTSW 4 122,742,216 (GRCm39) splice site probably benign
R0646:Ppt1 UTSW 4 122,737,892 (GRCm39) missense probably benign
R1542:Ppt1 UTSW 4 122,751,402 (GRCm39) missense probably benign
R1938:Ppt1 UTSW 4 122,739,784 (GRCm39) missense probably damaging 1.00
R3103:Ppt1 UTSW 4 122,730,100 (GRCm39) missense probably benign 0.00
R4862:Ppt1 UTSW 4 122,738,242 (GRCm39) missense probably damaging 1.00
R7753:Ppt1 UTSW 4 122,730,131 (GRCm39) missense possibly damaging 0.50
R9483:Ppt1 UTSW 4 122,751,367 (GRCm39) missense possibly damaging 0.58
X0020:Ppt1 UTSW 4 122,738,227 (GRCm39) missense possibly damaging 0.87
X0035:Ppt1 UTSW 4 122,742,311 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- AACGTCTCTGTCAGGATGCAG -3'
(R):5'- ACTGCTGCCAGGATTTTAACAAAG -3'

Sequencing Primer
(F):5'- TCTGTCAGGATGCAGAGCCC -3'
(R):5'- AAAGACACCTGGTTGTCGTC -3'
Posted On 2019-11-12