Mutagenetix > Incidental Mutation

Incidental Mutation 'R1646:Pdlim4'

173895

Institutional Source

Beutler Lab

Gene Symbol

Pdlim4

Ensembl Gene

ENSMUSG00000020388

Gene Name

PDZ and LIM domain 4

Synonyms

Ril

MMRRC Submission

039682-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.191) question?

Stock #

R1646 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

54054928-54069014 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 54056254 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 132 (L132Q)

Ref Sequence

ENSEMBL: ENSMUSP00000090797 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018755] [ENSMUST00000093109] [ENSMUST00000144477]

AlphaFold

P70271

Predicted Effect

possibly damaging
Transcript: ENSMUST00000018755
AA Change: L132Q

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000018755
Gene: ENSMUSG00000020388
AA Change: L132Q

Domain	Start	End	E-Value	Type
PDZ	11	84	1.05e-17	SMART
Pfam:DUF4749	142	230	7.2e-14	PFAM
LIM	254	305	9.75e-18	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000093109
AA Change: L132Q

PolyPhen 2 Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000090797
Gene: ENSMUSG00000020388
AA Change: L132Q

Domain	Start	End	E-Value	Type
PDZ	11	84	1.05e-17	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127271

Predicted Effect

possibly damaging
Transcript: ENSMUST00000144477
AA Change: L73Q

PolyPhen 2 Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000121248
Gene: ENSMUSG00000020388
AA Change: L73Q

Domain	Start	End	E-Value	Type
Blast:PDZ	1	25	2e-10	BLAST
SCOP:d1qava_	1	25	3e-4	SMART
PDB:2V1W\|B	1	28	2e-11	PDB

Meta Mutation Damage Score

0.0851

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.1%
20x: 91.8%

Validation Efficiency

96% (69/72)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein which may be involved in bone development. Mutations in this gene are associated with susceptibility to osteoporosis. [provided by RefSeq, Nov 2009]

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5330417C22Rik	A	T	3: 108,462,990	S751T	probably damaging	Het
Akna	T	G	4: 63,383,892	I581L	probably benign	Het
Cacnb4	A	G	2: 52,474,900	I117T	possibly damaging	Het
Capn1	A	T	19: 5,997,730	F434L	probably benign	Het
Cbs	T	C	17: 31,613,195	T547A	probably benign	Het
Col6a5	A	T	9: 105,862,749	L2557*	probably null	Het
D17Wsu92e	A	G	17: 27,793,960	S88P	probably damaging	Het
D1Ertd622e	A	T	1: 97,645,806	I178N	probably damaging	Het
Dach1	A	G	14: 98,169,114	S66P	unknown	Het
Ddx31	T	C	2: 28,892,520	V625A	probably benign	Het
Dmxl1	T	G	18: 49,962,261	V2969G	probably damaging	Het
Eapp	T	A	12: 54,685,960	K122*	probably null	Het
Epb41l5	G	T	1: 119,550,022		probably benign	Het
Fat1	T	C	8: 45,018,042	S1628P	probably damaging	Het
Fgfr2	T	A	7: 130,242,644	E37V	probably damaging	Het
Fgfr4	A	T	13: 55,165,964	N529Y	probably damaging	Het
Fsip2	A	T	2: 82,978,517	T1727S	probably benign	Het
Gak	A	T	5: 108,602,854	S397T	probably damaging	Het
Gm6040	T	A	8: 20,917,097	I36F	possibly damaging	Het
Grhl1	A	G	12: 24,611,861	D513G	possibly damaging	Het
Gstt1	T	A	10: 75,784,106	D219V	possibly damaging	Het
Hcfc2	T	G	10: 82,701,027	V91G	probably damaging	Het
Hells	A	T	19: 38,967,783	I808L	probably benign	Het
Icmt	T	A	4: 152,299,715	V110E	possibly damaging	Het
Iqca	C	T	1: 90,140,038	V164M	probably damaging	Het
Klri1	G	A	6: 129,703,336	P119S	probably benign	Het
Krt71	C	A	15: 101,738,764		probably null	Het
Lpin1	A	G	12: 16,573,658		probably null	Het
Metap2	T	C	10: 93,870,197	H241R	probably damaging	Het
Myh15	A	G	16: 49,195,568	Y1869C	probably damaging	Het
Myo1h	G	A	5: 114,317,632	G59E	possibly damaging	Het
Ncam2	T	G	16: 81,465,706		probably benign	Het
Npat	T	C	9: 53,555,134	V241A	probably benign	Het
Npbwr1	C	A	1: 5,917,254	V14L	probably benign	Het
Nup37	T	A	10: 88,178,234	V323E	possibly damaging	Het
Olfr1036	A	G	2: 86,075,616	N292S	probably damaging	Het
Olfr1351	C	A	10: 79,017,506	Y61*	probably null	Het
Olfr483	C	T	7: 108,103,591	T94I	probably benign	Het
Olfr743	A	T	14: 50,533,583	Q57L	probably benign	Het
Ptcd3	T	C	6: 71,898,395	D201G	probably benign	Het
Ptk7	A	T	17: 46,586,297	F370I	probably benign	Het
Pus7l	T	C	15: 94,533,636	N371D	probably benign	Het
Pzp	G	A	6: 128,503,555	A589V	probably benign	Het
Rasef	T	A	4: 73,734,549	R572W	probably damaging	Het
Reep5	T	C	18: 34,349,659	T166A	probably benign	Het
Rhov	A	G	2: 119,271,020	V35A	probably damaging	Het
Ripk4	C	T	16: 97,743,897	G517R	probably damaging	Het
Rnasel	A	G	1: 153,755,054	T439A	probably damaging	Het
Slamf9	A	G	1: 172,477,340	T174A	probably benign	Het
Slc12a9	A	G	5: 137,323,149	L414P	probably damaging	Het
Slf1	G	A	13: 77,066,648	R640*	probably null	Het
Slfn8	G	T	11: 83,016,886	P277Q	probably damaging	Het
Stpg2	T	A	3: 139,419,702		probably benign	Het
Tm9sf3	A	C	19: 41,223,179	N408K	possibly damaging	Het
Trio	A	G	15: 27,758,347	V2049A	possibly damaging	Het
Ttn	A	T	2: 76,814,733	I11180N	probably damaging	Het
Ush2a	T	C	1: 188,415,821	C982R	probably damaging	Het
Usp36	C	T	11: 118,273,566	V207M	probably damaging	Het
Uvrag	T	C	7: 99,118,224	T67A	probably damaging	Het
Vasp	G	A	7: 19,260,978		probably benign	Het
Vmn2r115	T	C	17: 23,359,539	F662S	probably damaging	Het
Vmn2r54	A	T	7: 12,632,507	C167S	probably damaging	Het
Vmn2r71	C	A	7: 85,621,268	N547K	probably damaging	Het
Wasf2	A	G	4: 133,176,591	I37V	probably benign	Het
Wwc2	T	C	8: 47,842,902	E1111G	unknown	Het
Zfp317	A	G	9: 19,647,312	Y274C	probably damaging	Het
Zhx3	T	C	2: 160,781,275	Y324C	probably damaging	Het
Zzef1	T	C	11: 72,864,036		probably null	Het

Other mutations in Pdlim4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01377:Pdlim4	APN	11	54,056,304 (GRCm38)	missense	probably benign	0.43
IGL02005:Pdlim4	APN	11	54,059,984 (GRCm38)	missense	probably benign	0.10
IGL02305:Pdlim4	APN	11	54,055,933 (GRCm38)	missense	probably damaging	1.00
IGL03073:Pdlim4	APN	11	54,063,641 (GRCm38)	missense	probably damaging	1.00
BB001:Pdlim4	UTSW	11	54,055,222 (GRCm38)	nonsense	probably null
BB011:Pdlim4	UTSW	11	54,055,222 (GRCm38)	nonsense	probably null
R0008:Pdlim4	UTSW	11	54,055,049 (GRCm38)	missense	probably damaging	1.00
R0612:Pdlim4	UTSW	11	54,068,887 (GRCm38)	missense	probably damaging	1.00
R1754:Pdlim4	UTSW	11	54,055,873 (GRCm38)	missense	possibly damaging	0.82
R2132:Pdlim4	UTSW	11	54,063,737 (GRCm38)	missense	possibly damaging	0.70
R3037:Pdlim4	UTSW	11	54,056,257 (GRCm38)	missense	probably benign	0.15
R4210:Pdlim4	UTSW	11	54,055,918 (GRCm38)	missense	possibly damaging	0.70
R5787:Pdlim4	UTSW	11	54,055,216 (GRCm38)	missense	probably damaging	1.00
R5969:Pdlim4	UTSW	11	54,063,656 (GRCm38)	missense	possibly damaging	0.50
R6862:Pdlim4	UTSW	11	54,055,848 (GRCm38)	missense	probably damaging	1.00
R7924:Pdlim4	UTSW	11	54,055,222 (GRCm38)	nonsense	probably null
R8927:Pdlim4	UTSW	11	54,059,964 (GRCm38)	missense	probably benign	0.01
R8928:Pdlim4	UTSW	11	54,059,964 (GRCm38)	missense	probably benign	0.01
R9023:Pdlim4	UTSW	11	54,068,836 (GRCm38)	unclassified	probably benign
R9026:Pdlim4	UTSW	11	54,055,454 (GRCm38)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GGAAAGCCAGCATGGTAATTCCAGC -3'
(R):5'- ACCTCAGACTTCCCTTGGAAGGAC -3'

Sequencing Primer
(F):5'- TGAGGCTCTTAGATCAAACGAC -3'
(R):5'- CCCTTCTGACTGTAGAATACGAG -3'

Posted On

2014-04-24