Mutagenetix > Incidental Mutation

Incidental Mutation 'R6908:Pkd2l1'

538899

Institutional Source

Beutler Lab

Gene Symbol

Pkd2l1

Ensembl Gene

ENSMUSG00000037578

Gene Name

polycystic kidney disease 2-like 1

Synonyms

PCL, PKD2L, Pkdl, polycystin-L, TRPP3

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.081) question?

Stock #

R6908 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

44147637-44192442 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 44152446 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 559 (I559T)

Ref Sequence

ENSEMBL: ENSMUSP00000045675 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000042026]

AlphaFold

A2A259

Predicted Effect

probably damaging
Transcript: ENSMUST00000042026
AA Change: I559T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000045675
Gene: ENSMUSG00000037578
AA Change: I559T

Domain	Start	End	E-Value	Type
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

Meta Mutation Damage Score

0.6228

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.2%

Validation Efficiency

95% (52/55)

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abi3bp	T	C	16: 56,657,305	I1197T	probably benign	Het
Atp2a1	A	G	7: 126,448,535		probably null	Het
B3glct	T	C	5: 149,696,476		probably null	Het
Bbs9	T	G	9: 22,567,723	I154S	probably damaging	Het
Brip1	T	C	11: 86,077,884	Y825C	probably damaging	Het
Ccdc186	A	T	19: 56,791,939		probably null	Het
Celf6	T	C	9: 59,603,823	V349A	probably benign	Het
Chd9	A	G	8: 90,956,416	T495A	probably benign	Het
Cxxc1	G	A	18: 74,220,559	C546Y	probably damaging	Het
Cxxc5	T	C	18: 35,859,215	V223A	probably damaging	Het
Dlc1	A	G	8: 36,937,687	F316S	probably benign	Het
Dnajc12	C	A	10: 63,397,325	Q82K	probably benign	Het
Dock8	G	A	19: 25,188,382	E1877K	probably damaging	Het
Epha3	T	G	16: 63,598,249	H611P	probably damaging	Het
Fpr-rs6	C	A	17: 20,182,439	C220F	probably damaging	Het
Fryl	A	G	5: 73,022,211	L2951P	probably damaging	Het
Gbp10	T	G	5: 105,221,032	T314P	probably damaging	Het
Hbb-bs	T	C	7: 103,827,534	N77D	probably benign	Het
Ints13	A	T	6: 146,555,033	D438E	probably damaging	Het
Itgb6	C	T	2: 60,650,021	V324M	probably benign	Het
Kdm7a	G	T	6: 39,144,439	L861M	possibly damaging	Het
Kirrel3	A	G	9: 35,013,401	T302A	possibly damaging	Het
Lama2	A	T	10: 27,031,196		probably null	Het
Lrp2	A	T	2: 69,472,365	C3007S	probably damaging	Het
Lypd3	G	C	7: 24,638,433	G75R	probably damaging	Het
Mastl	T	C	2: 23,155,976		probably benign	Het
Mcf2l	T	C	8: 13,018,919	V1087A	probably benign	Het
Mcmdc2	C	A	1: 9,930,778		probably null	Het
Ms4a3	A	G	19: 11,638,295	I39T	probably damaging	Het
Mylk	T	G	16: 34,880,273	C495G	probably benign	Het
Myo10	A	G	15: 25,804,383	D1588G	probably damaging	Het
Myo15	A	T	11: 60,506,006	T2634S	probably damaging	Het
Nlrp1b	T	C	11: 71,217,296	I460V	probably benign	Het
Nmt1	T	G	11: 103,058,254	S312A	possibly damaging	Het
Nynrin	T	G	14: 55,863,878	S335A	probably benign	Het
Olfr710	T	C	7: 106,944,632	Y123C	possibly damaging	Het
Paxip1	T	C	5: 27,791,224	Y19C	possibly damaging	Het
Pcdhb2	G	T	18: 37,296,524	A517S	probably damaging	Het
Plec	G	A	15: 76,185,881	Q806*	probably null	Het
Prss51	C	T	14: 64,096,152	A70V	probably benign	Het
Psd3	A	T	8: 67,964,177	I356K	probably benign	Het
Ptprn2	A	T	12: 116,888,888	I522F	probably benign	Het
Rab39	T	C	9: 53,706,069	D16G	probably damaging	Het
Ralgps1	T	C	2: 33,143,100	Q439R	probably benign	Het
Rapgef2	A	T	3: 79,104,063	D238E	probably benign	Het
Ripor2	G	A	13: 24,706,232	G697S	probably damaging	Het
Scn11a	A	T	9: 119,792,426	F642I	probably damaging	Het
Serinc4	G	A	2: 121,453,605	T310I	probably benign	Het
Sfpq	GCCGCCGCAGCAGCCTCCGCCGCAGCAGCC	GCCGCCGCAGCAGCC	4: 127,021,626		probably benign	Het
Slc36a3	T	C	11: 55,149,886		probably benign	Het
Smc1b	A	G	15: 85,107,010	S656P	probably damaging	Het
Sorbs1	A	G	19: 40,352,332	S455P	probably damaging	Het
Ttn	C	A	2: 76,889,858		probably benign	Het
Tyw5	T	C	1: 57,401,523	R27G	probably damaging	Het
Vmn1r209	T	C	13: 22,806,230	T97A	possibly damaging	Het

Other mutations in Pkd2l1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00420:Pkd2l1	APN	19	44157636	critical splice donor site	probably null
IGL00426:Pkd2l1	APN	19	44155605	missense	probably benign	0.21
IGL00848:Pkd2l1	APN	19	44192279	utr 5 prime	probably benign
IGL01315:Pkd2l1	APN	19	44192196	missense	probably benign	0.09
IGL01654:Pkd2l1	APN	19	44154223	missense	probably damaging	0.98
IGL01786:Pkd2l1	APN	19	44191442	missense	probably damaging	0.96
IGL02174:Pkd2l1	APN	19	44157268	missense	probably benign	0.04
IGL02648:Pkd2l1	APN	19	44155536	missense	possibly damaging	0.72
R0654:Pkd2l1	UTSW	19	44157631	splice site	probably null
R0762:Pkd2l1	UTSW	19	44150470	missense	probably benign	0.19
R0981:Pkd2l1	UTSW	19	44154422	critical splice donor site	probably null
R1114:Pkd2l1	UTSW	19	44191544	splice site	probably benign
R1381:Pkd2l1	UTSW	19	44150463	missense	probably benign	0.08
R1467:Pkd2l1	UTSW	19	44154209	missense	possibly damaging	0.91
R1467:Pkd2l1	UTSW	19	44154209	missense	possibly damaging	0.91
R1754:Pkd2l1	UTSW	19	44155601	nonsense	probably null
R2009:Pkd2l1	UTSW	19	44155964	missense	probably benign	0.01
R2125:Pkd2l1	UTSW	19	44154500	missense	possibly damaging	0.91
R2696:Pkd2l1	UTSW	19	44157269	missense	probably benign	0.01
R3001:Pkd2l1	UTSW	19	44155557	missense	possibly damaging	0.81
R3002:Pkd2l1	UTSW	19	44155557	missense	possibly damaging	0.81
R3701:Pkd2l1	UTSW	19	44157227	missense	probably damaging	0.99
R4179:Pkd2l1	UTSW	19	44192181	missense	probably benign	0.01
R4180:Pkd2l1	UTSW	19	44192181	missense	probably benign	0.01
R4614:Pkd2l1	UTSW	19	44154134	missense	probably damaging	0.99
R4616:Pkd2l1	UTSW	19	44154134	missense	probably damaging	0.99
R4617:Pkd2l1	UTSW	19	44154134	missense	probably damaging	0.99
R4618:Pkd2l1	UTSW	19	44154134	missense	probably damaging	0.99
R4762:Pkd2l1	UTSW	19	44155621	missense	probably benign	0.09
R4893:Pkd2l1	UTSW	19	44153771	missense	probably benign	0.00
R4907:Pkd2l1	UTSW	19	44154142	missense	possibly damaging	0.95
R5004:Pkd2l1	UTSW	19	44149577	missense	probably benign	0.00
R5380:Pkd2l1	UTSW	19	44157732	missense	probably benign	0.33
R5480:Pkd2l1	UTSW	19	44192156	missense	probably benign	0.18
R5950:Pkd2l1	UTSW	19	44152090	missense	probably benign	0.27
R6248:Pkd2l1	UTSW	19	44157669	missense	probably benign	0.00
R6925:Pkd2l1	UTSW	19	44191508	missense	possibly damaging	0.92
R7021:Pkd2l1	UTSW	19	44154208	missense	probably damaging	0.98
R7322:Pkd2l1	UTSW	19	44157690	missense	probably benign	0.00
R7378:Pkd2l1	UTSW	19	44153715	missense	probably benign	0.05
R7442:Pkd2l1	UTSW	19	44157229	missense	probably benign	0.01
R7636:Pkd2l1	UTSW	19	44191431	missense	possibly damaging	0.70
R7954:Pkd2l1	UTSW	19	44154212	missense	probably benign	0.15
R7989:Pkd2l1	UTSW	19	44154068	missense	probably benign	0.10
R9007:Pkd2l1	UTSW	19	44152425	missense	possibly damaging	0.49
R9245:Pkd2l1	UTSW	19	44155455	missense	probably benign	0.33
R9675:Pkd2l1	UTSW	19	44149257	missense	probably benign	0.00
X0026:Pkd2l1	UTSW	19	44157182	missense	probably damaging	1.00
Z1176:Pkd2l1	UTSW	19	44149271	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AGGCATTCAAGAGCACAGGC -3'
(R):5'- AAGAGGCTCAGTGCTTTTAGTG -3'

Sequencing Primer
(F):5'- GGCGCCTGCACCAATCAAG -3'
(R):5'- TTTGGAGGTAAAAACCTAGGTCAC -3'

Posted On

2018-11-06