Incidental Mutation 'R4617:Pkd2l1'
ID 351140
Institutional Source Beutler Lab
Gene Symbol Pkd2l1
Ensembl Gene ENSMUSG00000037578
Gene Name polycystic kidney disease 2-like 1
Synonyms PKD2L, polycystin-L, PCL, TRPP3, Pkdl
MMRRC Submission 041828-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.087) question?
Stock # R4617 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 44136076-44180881 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 44142573 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 490 (A490S)
Ref Sequence ENSEMBL: ENSMUSP00000045675 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000042026]
AlphaFold A2A259
Predicted Effect probably damaging
Transcript: ENSMUST00000042026
AA Change: A490S

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000045675
Gene: ENSMUSG00000037578
AA Change: A490S

DomainStartEndE-ValueType
transmembrane domain 105 127 N/A INTRINSIC
Pfam:PKD_channel 145 567 1.3e-172 PFAM
Pfam:Ion_trans 335 572 1.8e-30 PFAM
low complexity region 592 598 N/A INTRINSIC
SCOP:d2pvba_ 616 676 2e-4 SMART
PDB:4GIF|A 698 739 1e-17 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161357
Meta Mutation Damage Score 0.4214 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 94.9%
Validation Efficiency 96% (66/69)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the polycystin protein family. The encoded protein contains multiple transmembrane domains, and cytoplasmic N- and C-termini. The protein may be an integral membrane protein involved in cell-cell/matrix interactions. This protein functions as a calcium-regulated nonselective cation channel. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit decreased chorda tympani nerve response to sour tastants. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 T C 1: 71,369,493 (GRCm39) I363V probably benign Het
Acaa1a T A 9: 119,178,006 (GRCm39) S279R probably damaging Het
Akr1cl A G 1: 65,060,550 (GRCm39) C156R probably damaging Het
Arhgap11a G A 2: 113,664,423 (GRCm39) T620M probably benign Het
Brinp1 A G 4: 68,681,198 (GRCm39) I444T possibly damaging Het
Ccdc150 A G 1: 54,394,913 (GRCm39) I760V probably benign Het
Cdh26 G A 2: 178,102,435 (GRCm39) probably benign Het
Cpd A G 11: 76,731,441 (GRCm39) L255P probably damaging Het
Cyfip2 A G 11: 46,144,845 (GRCm39) Y670H probably damaging Het
Disp2 G A 2: 118,620,643 (GRCm39) M458I probably benign Het
Dot1l T C 10: 80,620,918 (GRCm39) I563T probably damaging Het
Egf A T 3: 129,484,442 (GRCm39) S1001T probably benign Het
Elfn1 A G 5: 139,957,764 (GRCm39) Y256C probably damaging Het
Exoc4 C T 6: 33,839,139 (GRCm39) T725I probably benign Het
Fam168b A G 1: 34,859,063 (GRCm39) V72A possibly damaging Het
Fbxw20 C T 9: 109,046,631 (GRCm39) S443N probably damaging Het
Flacc1 A T 1: 58,700,601 (GRCm39) D301E probably benign Het
Flrt2 T C 12: 95,747,003 (GRCm39) V447A possibly damaging Het
Gm4846 A G 1: 166,323,550 (GRCm39) S58P probably damaging Het
Gpr20 T C 15: 73,567,585 (GRCm39) N268S probably benign Het
Lpcat2b T C 5: 107,581,865 (GRCm39) L398P possibly damaging Het
Mapk8ip3 G A 17: 25,123,761 (GRCm39) P587L probably damaging Het
Mfap4 C A 11: 61,376,335 (GRCm39) probably benign Het
Mplkipl1 C T 19: 61,164,364 (GRCm39) G24R unknown Het
Mrpl38 T C 11: 116,023,278 (GRCm39) D325G probably damaging Het
Mtmr12 A G 15: 12,270,132 (GRCm39) E430G probably damaging Het
Mup18 T A 4: 61,590,154 (GRCm39) I125F possibly damaging Het
Ogdhl A G 14: 32,047,842 (GRCm39) R31G probably benign Het
Or13f5 A T 4: 52,825,399 (GRCm39) M1L probably benign Het
Pcdh1 C A 18: 38,330,913 (GRCm39) V697L probably benign Het
Pcdhga9 T C 18: 37,871,553 (GRCm39) Y461H probably damaging Het
Pdzrn4 A G 15: 92,667,723 (GRCm39) Y625C probably damaging Het
Poglut2 A C 1: 44,149,180 (GRCm39) F453V probably damaging Het
Ptprn T A 1: 75,228,931 (GRCm39) D828V possibly damaging Het
Rgs12 T A 5: 35,177,700 (GRCm39) W97R probably damaging Het
Rnf10 T A 5: 115,386,762 (GRCm39) Q508L probably damaging Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Sec24b A T 3: 129,834,413 (GRCm39) S126T possibly damaging Het
Slc6a5 A G 7: 49,561,768 (GRCm39) N100S probably benign Het
Speer1j T C 5: 11,553,798 (GRCm39) S7P probably benign Het
Stam2 A T 2: 52,605,716 (GRCm39) D167E probably benign Het
Stambp G A 6: 83,538,960 (GRCm39) Q147* probably null Het
Tbc1d32 A G 10: 56,047,000 (GRCm39) V556A possibly damaging Het
Tll2 T C 19: 41,087,075 (GRCm39) D592G probably benign Het
Tmem199 A T 11: 78,400,508 (GRCm39) probably benign Het
Traip T A 9: 107,847,218 (GRCm39) N352K probably benign Het
Trmt1l C T 1: 151,329,799 (GRCm39) Q581* probably null Het
Usp54 C A 14: 20,600,406 (GRCm39) A1444S probably benign Het
Vsig1 G T X: 139,827,135 (GRCm39) A95S probably benign Het
Xdh G A 17: 74,225,389 (GRCm39) T471I probably damaging Het
Zdhhc19 A G 16: 32,316,494 (GRCm39) D83G probably damaging Het
Zfp352 A G 4: 90,113,318 (GRCm39) K486R probably benign Het
Zfp451 A G 1: 33,841,752 (GRCm39) probably benign Het
Zfp963 A T 8: 70,195,944 (GRCm39) S170T probably benign Het
Zfp970 A G 2: 177,167,961 (GRCm39) I512V probably benign Het
Zfp990 A G 4: 145,263,616 (GRCm39) I205V possibly damaging Het
Other mutations in Pkd2l1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00420:Pkd2l1 APN 19 44,146,075 (GRCm39) critical splice donor site probably null
IGL00426:Pkd2l1 APN 19 44,144,044 (GRCm39) missense probably benign 0.21
IGL00848:Pkd2l1 APN 19 44,180,718 (GRCm39) utr 5 prime probably benign
IGL01315:Pkd2l1 APN 19 44,180,635 (GRCm39) missense probably benign 0.09
IGL01654:Pkd2l1 APN 19 44,142,662 (GRCm39) missense probably damaging 0.98
IGL01786:Pkd2l1 APN 19 44,179,881 (GRCm39) missense probably damaging 0.96
IGL02174:Pkd2l1 APN 19 44,145,707 (GRCm39) missense probably benign 0.04
IGL02648:Pkd2l1 APN 19 44,143,975 (GRCm39) missense possibly damaging 0.72
R0654:Pkd2l1 UTSW 19 44,146,070 (GRCm39) splice site probably null
R0762:Pkd2l1 UTSW 19 44,138,909 (GRCm39) missense probably benign 0.19
R0981:Pkd2l1 UTSW 19 44,142,861 (GRCm39) critical splice donor site probably null
R1114:Pkd2l1 UTSW 19 44,179,983 (GRCm39) splice site probably benign
R1381:Pkd2l1 UTSW 19 44,138,902 (GRCm39) missense probably benign 0.08
R1467:Pkd2l1 UTSW 19 44,142,648 (GRCm39) missense possibly damaging 0.91
R1467:Pkd2l1 UTSW 19 44,142,648 (GRCm39) missense possibly damaging 0.91
R1754:Pkd2l1 UTSW 19 44,144,040 (GRCm39) nonsense probably null
R2009:Pkd2l1 UTSW 19 44,144,403 (GRCm39) missense probably benign 0.01
R2125:Pkd2l1 UTSW 19 44,142,939 (GRCm39) missense possibly damaging 0.91
R2696:Pkd2l1 UTSW 19 44,145,708 (GRCm39) missense probably benign 0.01
R3001:Pkd2l1 UTSW 19 44,143,996 (GRCm39) missense possibly damaging 0.81
R3002:Pkd2l1 UTSW 19 44,143,996 (GRCm39) missense possibly damaging 0.81
R3701:Pkd2l1 UTSW 19 44,145,666 (GRCm39) missense probably damaging 0.99
R4179:Pkd2l1 UTSW 19 44,180,620 (GRCm39) missense probably benign 0.01
R4180:Pkd2l1 UTSW 19 44,180,620 (GRCm39) missense probably benign 0.01
R4614:Pkd2l1 UTSW 19 44,142,573 (GRCm39) missense probably damaging 0.99
R4616:Pkd2l1 UTSW 19 44,142,573 (GRCm39) missense probably damaging 0.99
R4618:Pkd2l1 UTSW 19 44,142,573 (GRCm39) missense probably damaging 0.99
R4762:Pkd2l1 UTSW 19 44,144,060 (GRCm39) missense probably benign 0.09
R4893:Pkd2l1 UTSW 19 44,142,210 (GRCm39) missense probably benign 0.00
R4907:Pkd2l1 UTSW 19 44,142,581 (GRCm39) missense possibly damaging 0.95
R5004:Pkd2l1 UTSW 19 44,138,016 (GRCm39) missense probably benign 0.00
R5380:Pkd2l1 UTSW 19 44,146,171 (GRCm39) missense probably benign 0.33
R5480:Pkd2l1 UTSW 19 44,180,595 (GRCm39) missense probably benign 0.18
R5950:Pkd2l1 UTSW 19 44,140,529 (GRCm39) missense probably benign 0.27
R6248:Pkd2l1 UTSW 19 44,146,108 (GRCm39) missense probably benign 0.00
R6908:Pkd2l1 UTSW 19 44,140,885 (GRCm39) missense probably damaging 1.00
R6925:Pkd2l1 UTSW 19 44,179,947 (GRCm39) missense possibly damaging 0.92
R7021:Pkd2l1 UTSW 19 44,142,647 (GRCm39) missense probably damaging 0.98
R7322:Pkd2l1 UTSW 19 44,146,129 (GRCm39) missense probably benign 0.00
R7378:Pkd2l1 UTSW 19 44,142,154 (GRCm39) missense probably benign 0.05
R7442:Pkd2l1 UTSW 19 44,145,668 (GRCm39) missense probably benign 0.01
R7636:Pkd2l1 UTSW 19 44,179,870 (GRCm39) missense possibly damaging 0.70
R7954:Pkd2l1 UTSW 19 44,142,651 (GRCm39) missense probably benign 0.15
R7989:Pkd2l1 UTSW 19 44,142,507 (GRCm39) missense probably benign 0.10
R9007:Pkd2l1 UTSW 19 44,140,864 (GRCm39) missense possibly damaging 0.49
R9245:Pkd2l1 UTSW 19 44,143,894 (GRCm39) missense probably benign 0.33
R9675:Pkd2l1 UTSW 19 44,137,696 (GRCm39) missense probably benign 0.00
X0026:Pkd2l1 UTSW 19 44,145,621 (GRCm39) missense probably damaging 1.00
Z1176:Pkd2l1 UTSW 19 44,137,710 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- TGGGGAAATTACTCGAGAGC -3'
(R):5'- TCTGTCCGTTCCTGGAGTAGTC -3'

Sequencing Primer
(F):5'- GCAGCTGCACTCAGATACCTTTAAG -3'
(R):5'- CCGTTCCTGGAGTAGTCTATGC -3'
Posted On 2015-10-08