Mutagenetix > Incidental Mutation

Incidental Mutation 'R4907:Pkd2l1'

379146

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

042509-MU

Accession Numbers

Essential gene?

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

Stock #

R4907 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

44136076-44180881 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 44142581 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 487 (V487A)

Ref Sequence

ENSEMBL: ENSMUSP00000045675 (fasta)

Gene Model

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

AlphaFold

A2A259

Predicted Effect

possibly damaging
Transcript: ENSMUST00000042026
AA Change: V487A

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000045675
Gene: ENSMUSG00000037578
AA Change: V487A

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

0.5676

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.9%
20x: 91.1%

Validation Efficiency

98% (89/91)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700066M21Rik	G	T	1: 57,422,350 (GRCm39)	G242V	probably damaging	Het
4933412E24Rik	T	C	15: 59,887,957 (GRCm39)	E161G	probably benign	Het
Abcc5	A	G	16: 20,195,296 (GRCm39)	S734P	possibly damaging	Het
Actn1	T	G	12: 80,228,188 (GRCm39)	H394P	probably damaging	Het
Adam8	A	T	7: 139,569,286 (GRCm39)	D144E	probably benign	Het
Ankrd50	A	T	3: 38,510,824 (GRCm39)	N514K	probably damaging	Het
Ankrd50	T	A	3: 38,509,122 (GRCm39)	K1082*	probably null	Het
Atp4a	A	G	7: 30,418,517 (GRCm39)	I602V	possibly damaging	Het
Baz2a	A	G	10: 127,946,677 (GRCm39)	T64A	probably damaging	Het
Btbd19	A	G	4: 116,977,764 (GRCm39)		probably benign	Het
Casz1	T	A	4: 149,028,998 (GRCm39)	S1148T	probably damaging	Het
Ccdc18	T	A	5: 108,284,007 (GRCm39)	D103E	probably benign	Het
Cd209d	T	C	8: 3,927,948 (GRCm39)	N52S	probably benign	Het
Cdh20	T	A	1: 110,066,053 (GRCm39)	Y776N	probably damaging	Het
Cdk14	A	G	5: 5,299,140 (GRCm39)	V101A	probably damaging	Het
Cldn22	T	C	8: 48,277,742 (GRCm39)	V60A	probably benign	Het
Clec10a	G	A	11: 70,060,797 (GRCm39)	G183D	probably benign	Het
Cnga3	T	C	1: 37,281,023 (GRCm39)		probably null	Het
Cts3	A	T	13: 61,714,634 (GRCm39)	F224I	probably benign	Het
Dync2i2	A	G	2: 29,922,472 (GRCm39)		probably null	Het
Fbxo40	A	G	16: 36,790,064 (GRCm39)	Y349H	probably benign	Het
Flt1	C	A	5: 147,620,749 (GRCm39)	A132S	probably benign	Het
Gm10029	A	T	13: 6,712,592 (GRCm39)		noncoding transcript	Het
Gm14399	T	A	2: 174,973,182 (GRCm39)		probably benign	Het
Gm9932	T	C	5: 100,347,014 (GRCm39)		noncoding transcript	Het
Immp1l	A	G	2: 105,767,462 (GRCm39)	Y107C	probably damaging	Het
Ism1	G	T	2: 139,520,672 (GRCm39)	G28V	probably benign	Het
Klf1	C	A	8: 85,629,814 (GRCm39)	S213*	probably null	Het
Krt12	T	C	11: 99,309,188 (GRCm39)	E329G	probably damaging	Het
Lama2	A	T	10: 27,040,942 (GRCm39)	N1460K	probably benign	Het
Llgl2	T	A	11: 115,744,800 (GRCm39)	Y932*	probably null	Het
Lrrc7	T	C	3: 157,866,877 (GRCm39)	I955V	probably damaging	Het
Ltbp1	A	G	17: 75,312,899 (GRCm39)	R7G	probably benign	Het
Mcm3ap	A	G	10: 76,329,275 (GRCm39)	E1152G	probably damaging	Het
Mgam2-ps	T	C	6: 40,811,677 (GRCm39)		noncoding transcript	Het
Mical3	T	A	6: 120,984,259 (GRCm39)	M206L	probably benign	Het
Mndal	T	G	1: 173,690,256 (GRCm39)	N358T	probably damaging	Het
Nckap5	A	G	1: 125,953,889 (GRCm39)	S824P	possibly damaging	Het
Ndufb2	T	C	6: 39,573,554 (GRCm39)		probably benign	Het
Nfatc3	C	A	8: 106,806,359 (GRCm39)	H401Q	probably damaging	Het
Npas2	T	C	1: 39,401,066 (GRCm39)	V810A	unknown	Het
Nt5c2	A	G	19: 46,884,978 (GRCm39)	V245A	possibly damaging	Het
Or1j4	A	T	2: 36,740,270 (GRCm39)	I71F	probably benign	Het
Or4d5	A	T	9: 40,011,955 (GRCm39)	M277K	probably benign	Het
Or51ah3	A	G	7: 103,210,241 (GRCm39)	M186V	possibly damaging	Het
Or52h9	A	G	7: 104,202,518 (GRCm39)	R131G	probably damaging	Het
Or5b109	A	G	19: 13,212,157 (GRCm39)	D181G	probably damaging	Het
Otof	A	T	5: 30,536,005 (GRCm39)		probably null	Het
Pck1	C	T	2: 172,998,816 (GRCm39)	T358I	probably damaging	Het
Pclo	T	C	5: 14,730,065 (GRCm39)		probably benign	Het
Pgm2	T	A	5: 64,261,221 (GRCm39)	F238L	probably benign	Het
Pgr	G	A	9: 8,947,044 (GRCm39)		probably benign	Het
Pkd1l3	T	A	8: 110,367,475 (GRCm39)	V1224E	probably damaging	Het
Pkhd1	T	C	1: 20,279,450 (GRCm39)	D2956G	probably damaging	Het
Rexo2	A	T	9: 48,390,703 (GRCm39)		probably null	Het
Rgs22	T	A	15: 36,087,570 (GRCm39)	L573F	possibly damaging	Het
Rufy3	T	G	5: 88,732,051 (GRCm39)	I18S	possibly damaging	Het
Slc30a9	T	C	5: 67,503,505 (GRCm39)	L393P	probably damaging	Het
Snw1	T	C	12: 87,506,259 (GRCm39)	I214V	probably benign	Het
Sorbs1	G	A	19: 40,328,491 (GRCm39)	Q595*	probably null	Het
Spata21	T	A	4: 140,824,432 (GRCm39)		probably null	Het
Ss18l1	G	T	2: 179,705,192 (GRCm39)		probably null	Het
Tmem163	A	T	1: 127,447,107 (GRCm39)	L176H	probably damaging	Het
Tpd52	T	C	3: 9,009,668 (GRCm39)		probably null	Het
Tpsab1	T	A	17: 25,562,436 (GRCm39)	Y297F	possibly damaging	Het
Trim55	A	G	3: 19,728,538 (GRCm39)	T450A	probably benign	Het
Ttf1	C	T	2: 28,954,668 (GRCm39)	H11Y	possibly damaging	Het
Txndc11	A	T	16: 10,906,398 (GRCm39)	H377Q	probably benign	Het
Usp17la	A	G	7: 104,510,355 (GRCm39)	Y320C	probably damaging	Het
Vmn2r109	T	C	17: 20,770,348 (GRCm39)	N547D	probably damaging	Het
Vmn2r54	A	T	7: 12,350,150 (GRCm39)		probably null	Het
Wdr33	T	C	18: 32,040,046 (GRCm39)	*1331Q	probably null	Het
Wdr90	T	A	17: 26,079,624 (GRCm39)		probably benign	Het
Xpo7	T	C	14: 70,908,069 (GRCm39)	M903V	probably benign	Het
Zfhx3	T	A	8: 109,519,986 (GRCm39)	S369R	probably damaging	Het
Zfp808	T	C	13: 62,319,287 (GRCm39)	F172S	possibly damaging	Het
Zfp821	A	G	8: 110,450,625 (GRCm39)	E55G	probably benign	Het
Zfp964	T	C	8: 70,115,972 (GRCm39)	Y191H	possibly damaging	Het
Zfyve1	T	C	12: 83,621,646 (GRCm39)	T250A	probably damaging	Het

Other mutations in Pkd2l1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
R4617: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
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'- GCAGGTGGGGAAATTACTCG -3'
(R):5'- CCGTTCCTGGAGTAGTCTATGC -3'

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

Posted On

2016-04-15