Mutagenetix > Incidental Mutations

Incidental Mutation 'R4616:Pkd2l1'

351077

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

041827-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.087) question?

Stock #

R4616 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

44147637-44192442 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 44154134 bp

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]

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

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161357

Meta Mutation Damage Score

0.4214

Coding Region Coverage

1x: 99.4%
3x: 98.7%
10x: 97.4%
20x: 95.6%

Validation Efficiency

100% (64/64)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010111I01Rik	G	A	13: 63,298,751	E123K	probably damaging	Het
4931417E11Rik	A	G	6: 73,469,269	V99A	probably benign	Het
Acod1	C	T	14: 103,055,345	T435M	probably benign	Het
Adgrf5	T	C	17: 43,452,440	F1078L	probably benign	Het
Adh6a	A	T	3: 138,324,947	N110I	probably damaging	Het
Aldh16a1	T	C	7: 45,148,788		probably benign	Het
Arhgef17	A	G	7: 100,882,485	F1302S	probably damaging	Het
Bcl2a1a	C	T	9: 88,957,453	R135W	probably damaging	Het
Bpifa6	T	C	2: 153,982,988	S28P	possibly damaging	Het
C9	A	G	15: 6,491,463	D51G	probably damaging	Het
Cfb	T	A	17: 34,859,068	H962L	probably benign	Het
Chn2	G	A	6: 54,290,403	M292I	probably damaging	Het
Clec16a	T	A	16: 10,644,883		probably null	Het
Cyp1a1	T	C	9: 57,701,756	S307P	probably benign	Het
Dsg3	T	C	18: 20,531,559	V538A	probably benign	Het
Erbb3	G	A	10: 128,572,770	Q815*	probably null	Het
Fam90a1a	C	A	8: 21,963,846	Q406K	possibly damaging	Het
Frmd3	T	C	4: 74,187,872	V585A	probably benign	Het
Gm7102	C	T	19: 61,175,926	G24R	unknown	Het
Gm8214	T	C	1: 183,681,897		noncoding transcript	Het
Gpld1	G	A	13: 24,984,816	G771D	probably damaging	Het
Gpr20	T	C	15: 73,695,736	N268S	probably benign	Het
Gria2	A	T	3: 80,706,897	I612N	probably damaging	Het
Ifit1bl1	T	C	19: 34,594,610	E149G	probably damaging	Het
Ighv1-82	T	C	12: 115,952,660	T77A	probably benign	Het
Ighv2-9	G	T	12: 113,879,219	T76K	probably damaging	Het
Igkv6-13	A	T	6: 70,458,035	M1K	probably null	Het
Igkv8-21	A	T	6: 70,315,157	S34T	probably benign	Het
Itpr1	A	G	6: 108,481,223	N1985D	probably damaging	Het
Lama3	T	C	18: 12,504,397		probably null	Het
Lamc2	T	C	1: 153,166,169	Y73C	probably damaging	Het
Maff	A	G	15: 79,357,698	D105G	probably damaging	Het
Mep1a	C	T	17: 43,486,241	V312M	possibly damaging	Het
Mfap4	C	A	11: 61,485,509		probably benign	Het
Mrgbp	A	T	2: 180,585,314		silent	Het
Mtmr4	T	C	11: 87,610,935	L548S	probably damaging	Het
Myo7b	T	C	18: 32,003,487		probably null	Het
Myo9a	T	C	9: 59,821,649	I596T	probably damaging	Het
Olfr38	G	T	6: 42,762,418	R122L	probably benign	Het
Olfr594	C	T	7: 103,220,422	R235*	probably null	Het
Pcsk5	T	G	19: 17,560,750	Q904H	probably benign	Het
Pdzrn3	G	T	6: 101,152,009	H565Q	probably damaging	Het
Phkg2	C	T	7: 127,577,620	R61W	probably damaging	Het
Pomgnt1	T	A	4: 116,154,890	I337N	probably damaging	Het
Psmd3	T	C	11: 98,682,926	V66A	probably benign	Het
Ptger3	T	C	3: 157,567,294	S93P	probably damaging	Het
Rbm27	T	A	18: 42,301,775	D301E	probably damaging	Het
Rdh16	A	T	10: 127,801,513		probably null	Het
Slc35a5	A	T	16: 45,144,292	F193I	probably benign	Het
Slc4a4	A	G	5: 89,038,561	K167R	probably damaging	Het
Sort1	A	T	3: 108,355,541	T772S	possibly damaging	Het
Sptbn5	T	A	2: 120,048,757		noncoding transcript	Het
Stard5	G	T	7: 83,633,281		probably benign	Het
Tbc1d22a	A	G	15: 86,235,685	T61A	probably damaging	Het
Tox2	T	C	2: 163,320,647	L479P	probably damaging	Het
Usp53	A	T	3: 122,959,120	M80K	probably damaging	Het
Vmn1r209	A	T	13: 22,805,965	L185Q	probably damaging	Het
Vmn2r59	A	G	7: 42,012,438	I651T	probably benign	Het
Vsig1	G	T	X: 140,926,386	A95S	probably benign	Het
Zfhx4	T	C	3: 5,413,067	S3556P	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
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
R6908:Pkd2l1	UTSW	19	44152446	missense	probably damaging	1.00
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
X0026:Pkd2l1	UTSW	19	44157182	missense	probably damaging	1.00
Z1176:Pkd2l1	UTSW	19	44149271	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TGGGGAAATTACTCGAGAGC -3'
(R):5'- TCTGTCCGTTCCTGGAGTAG -3'

Sequencing Primer
(F):5'- GCAGCTGCACTCAGATACCTTTAAG -3'
(R):5'- CCGTTCCTGGAGTAGTCTATGC -3'

Posted On

2015-10-08