Mutagenetix > Incidental Mutation

Incidental Mutation 'R2005:Pdlim2'

225424

Institutional Source

Beutler Lab

Gene Symbol

Pdlim2

Ensembl Gene

ENSMUSG00000022090

Gene Name

PDZ and LIM domain 2

Synonyms

SLIM, 4732462F18Rik, mystique

MMRRC Submission

040014-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.074) question?

Stock #

R2005 (G1)

Quality Score

140

Status

Not validated

Chromosome

Chromosomal Location

70401667-70415130 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 70402228 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 296 (R296H)

Ref Sequence

ENSEMBL: ENSMUSP00000116200 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000022681] [ENSMUST00000127836] [ENSMUST00000129174] [ENSMUST00000143393] [ENSMUST00000153735]

AlphaFold

Q8R1G6

Predicted Effect

probably damaging
Transcript: ENSMUST00000022681
AA Change: R296H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000022681
Gene: ENSMUSG00000022090
AA Change: R296H

Domain	Start	End	E-Value	Type
PDZ	11	84	3.41e-17	SMART
low complexity region	129	144	N/A	INTRINSIC
Pfam:DUF4749	169	256	4.4e-12	PFAM
low complexity region	259	271	N/A	INTRINSIC
LIM	282	334	1.25e-6	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000125300
AA Change: R97H

SMART Domains

Protein: ENSMUSP00000116694
Gene: ENSMUSG00000022090
AA Change: R97H

Domain	Start	End	E-Value	Type
Pfam:DUF4749	7	58	6.4e-13	PFAM
low complexity region	61	73	N/A	INTRINSIC
LIM	84	136	1.25e-6	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000127836
AA Change: R75H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000141050
Gene: ENSMUSG00000022090
AA Change: R75H

Domain	Start	End	E-Value	Type
low complexity region	20	29	N/A	INTRINSIC
low complexity region	38	50	N/A	INTRINSIC
LIM	61	113	5.9e-9	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000129174
AA Change: R75H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000139820
Gene: ENSMUSG00000022090
AA Change: R75H

Domain	Start	End	E-Value	Type
low complexity region	20	29	N/A	INTRINSIC
low complexity region	38	50	N/A	INTRINSIC
LIM	61	113	5.9e-9	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135944

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141363

Predicted Effect

probably benign
Transcript: ENSMUST00000143393

SMART Domains

Protein: ENSMUSP00000119222
Gene: ENSMUSG00000022090

Domain	Start	End	E-Value	Type
PDZ	11	84	3.41e-17	SMART
low complexity region	129	144	N/A	INTRINSIC
low complexity region	199	210	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000153735
AA Change: R296H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000116200
Gene: ENSMUSG00000022090
AA Change: R296H

Domain	Start	End	E-Value	Type
PDZ	11	84	3.41e-17	SMART
low complexity region	129	144	N/A	INTRINSIC
low complexity region	199	210	N/A	INTRINSIC
low complexity region	241	250	N/A	INTRINSIC
low complexity region	259	271	N/A	INTRINSIC
LIM	282	334	1.25e-6	SMART

Meta Mutation Damage Score

0.8007

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.0%

Validation Efficiency

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 ALP subfamily of PDZ-LIM domain proteins. The encoded protein suppresses anchorage-dependent growth and promotes cell migration and adhesion through interactions with the actin cytoskeleton via the PDZ domain. The encoded protein is also a putative tumor suppressor protein, and decreased expression of this gene is associated with several malignancies including breast cancer and adult T-cell leukemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]
PHENOTYPE: Mice homozygous for a knock-out allele display increased IFN-gamma production by Th1 cells and an enhanced inflammatory response to in vivo challenge with heat-killed Listeria monocytogenes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb5	G	A	12: 118,841,562 (GRCm39)	A961V	probably benign	Het
Adcy10	A	G	1: 165,352,591 (GRCm39)	Y475C	probably benign	Het
Adgrb3	T	C	1: 25,150,799 (GRCm39)	M1145V	probably benign	Het
Akr1c21	A	G	13: 4,624,214 (GRCm39)	T23A	probably damaging	Het
Ankrd33b	A	T	15: 31,297,814 (GRCm39)	S314R	probably damaging	Het
Apc	T	C	18: 34,443,962 (GRCm39)		probably null	Het
Atg9a	T	A	1: 75,162,635 (GRCm39)	Q460L	probably benign	Het
Birc2	C	T	9: 7,860,342 (GRCm39)	C292Y	probably damaging	Het
Capn5	T	C	7: 97,778,570 (GRCm39)	I350V	probably benign	Het
Cc2d2a	G	A	5: 43,883,715 (GRCm39)		probably null	Het
Cdh22	T	A	2: 165,022,843 (GRCm39)	E76V	probably damaging	Het
Cdh8	T	C	8: 99,760,103 (GRCm39)		probably null	Het
Cdkn1b	ATTCTTCTTC	ATTCTTCTTCTTC	6: 134,898,919 (GRCm39)		probably benign	Het
Cfap54	T	A	10: 92,720,630 (GRCm39)	D2608V	unknown	Het
Crebrf	T	C	17: 26,961,857 (GRCm39)	V318A	possibly damaging	Het
Cwf19l2	A	T	9: 3,430,720 (GRCm39)	N351Y	possibly damaging	Het
Cyp2c67	A	T	19: 39,631,789 (GRCm39)	M136K	probably damaging	Het
Ddx10	A	G	9: 53,151,775 (GRCm39)		probably null	Het
Ddx47	A	G	6: 134,995,084 (GRCm39)	N92S	probably benign	Het
Ddx50	T	A	10: 62,476,243 (GRCm39)	H306L	probably benign	Het
Dnajc27	A	G	12: 4,147,317 (GRCm39)	T167A	possibly damaging	Het
Dscam	T	G	16: 96,840,120 (GRCm39)	K162N	probably benign	Het
Eif4h	G	A	5: 134,656,531 (GRCm39)	T53I	probably benign	Het
Elmo2	T	C	2: 165,140,199 (GRCm39)	N332S	probably benign	Het
Ergic3	A	G	2: 155,853,028 (GRCm39)	N157S	possibly damaging	Het
F2rl1	G	T	13: 95,649,782 (GRCm39)	R367S	probably damaging	Het
Fbxo36	G	A	1: 84,877,790 (GRCm39)	A151T	probably benign	Het
Foxf2	G	T	13: 31,810,124 (GRCm39)	R21L	unknown	Het
Gmip	T	A	8: 70,266,693 (GRCm39)	H269Q	probably benign	Het
Gng4	T	A	13: 13,980,751 (GRCm39)	V32E	probably benign	Het
Grm3	T	C	5: 9,639,793 (GRCm39)	Y84C	possibly damaging	Het
Helz2	C	T	2: 180,873,122 (GRCm39)	R2396H	probably benign	Het
Icosl	A	T	10: 77,907,787 (GRCm39)	M116L	possibly damaging	Het
Itgb3bp	A	C	4: 99,702,295 (GRCm39)	N16K	probably benign	Het
Kcnt2	A	G	1: 140,480,756 (GRCm39)	M824V	probably damaging	Het
Mki67	T	A	7: 135,300,238 (GRCm39)	K1599*	probably null	Het
Mmp25	G	A	17: 23,859,216 (GRCm39)	R144W	probably damaging	Het
Mmrn1	A	T	6: 60,953,068 (GRCm39)	I450F	possibly damaging	Het
Mroh2b	A	T	15: 4,946,640 (GRCm39)	K480M	probably damaging	Het
Nbn	T	A	4: 15,979,351 (GRCm39)	D445E	probably benign	Het
Npbwr1	T	A	1: 5,986,570 (GRCm39)	S315C	probably damaging	Het
Or10ag56	T	A	2: 87,139,792 (GRCm39)	S240T	probably benign	Het
Or1e19	A	T	11: 73,316,065 (GRCm39)	V248E	probably damaging	Het
Or5d38	A	G	2: 87,954,891 (GRCm39)	L146P	probably damaging	Het
Or7g16	G	A	9: 18,726,801 (GRCm39)	S263L	probably benign	Het
Pard3b	A	T	1: 62,184,050 (GRCm39)	E183D	probably benign	Het
Pde10a	G	A	17: 9,147,923 (GRCm39)		probably null	Het
Prdm13	T	C	4: 21,685,695 (GRCm39)		probably benign	Het
Rc3h2	T	A	2: 37,279,765 (GRCm39)	K461*	probably null	Het
Reep2	C	T	18: 34,978,674 (GRCm39)	T117M	probably damaging	Het
Rhbdd1	A	G	1: 82,318,531 (GRCm39)	N138S	probably benign	Het
Rnf19a	A	T	15: 36,241,916 (GRCm39)	F708I	possibly damaging	Het
Robo2	G	A	16: 73,730,003 (GRCm39)	H1069Y	possibly damaging	Het
Rpl9	C	T	5: 65,546,878 (GRCm39)	V112I	probably benign	Het
Sec16a	A	C	2: 26,329,092 (GRCm39)	S974R	probably benign	Het
Sfrp5	A	G	19: 42,187,275 (GRCm39)	M265T	probably benign	Het
Skint7	T	C	4: 111,842,047 (GRCm39)	I305T	probably benign	Het
Slc6a7	T	C	18: 61,134,713 (GRCm39)	D454G	possibly damaging	Het
Slco6c1	A	G	1: 97,009,214 (GRCm39)	I407T	probably damaging	Het
Slfn8	A	T	11: 82,894,976 (GRCm39)	M610K	probably damaging	Het
Spidr	A	G	16: 15,865,913 (GRCm39)	S299P	probably damaging	Het
Sptbn4	C	T	7: 27,065,844 (GRCm39)	W2034*	probably null	Het
Stard9	T	A	2: 120,495,426 (GRCm39)	F100L	possibly damaging	Het
Stard9	C	A	2: 120,504,117 (GRCm39)	S221R	probably damaging	Het
Stc1	T	C	14: 69,269,096 (GRCm39)		probably null	Het
Sun2	T	C	15: 79,610,825 (GRCm39)	E667G	possibly damaging	Het
Tacc2	T	C	7: 130,333,280 (GRCm39)	S511P	probably damaging	Het
Tasp1	T	G	2: 139,819,598 (GRCm39)	K202Q	probably damaging	Het
Tdrd6	A	G	17: 43,939,546 (GRCm39)	F501L	probably damaging	Het
Tgds	A	G	14: 118,368,068 (GRCm39)	V35A	possibly damaging	Het
Tubgcp6	G	A	15: 88,988,369 (GRCm39)	T860I	probably benign	Het
Twf1	C	T	15: 94,483,328 (GRCm39)		probably null	Het
Vangl1	A	G	3: 102,070,782 (GRCm39)	S385P	probably benign	Het
Vmn2r117	A	G	17: 23,696,618 (GRCm39)	I263T	probably damaging	Het
Washc5	A	G	15: 59,213,004 (GRCm39)	L892P	possibly damaging	Het
Wnk4	T	C	11: 101,154,716 (GRCm39)	C302R	probably damaging	Het
Zfp395	A	G	14: 65,626,334 (GRCm39)	E191G	possibly damaging	Het
Zkscan17	A	G	11: 59,383,042 (GRCm39)	L302P	probably damaging	Het

Other mutations in Pdlim2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02295:Pdlim2	APN	14	70,403,532 (GRCm39)	splice site	probably benign
IGL02338:Pdlim2	APN	14	70,411,906 (GRCm39)	missense	probably damaging	1.00
IGL03286:Pdlim2	APN	14	70,411,925 (GRCm39)	missense	possibly damaging	0.88
PIT4504001:Pdlim2	UTSW	14	70,403,579 (GRCm39)	missense	probably benign	0.44
R0751:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R0768:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R0832:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1167:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1207:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1207:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1343:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1412:Pdlim2	UTSW	14	70,411,773 (GRCm39)	splice site	probably benign
R1595:Pdlim2	UTSW	14	70,402,193 (GRCm39)	missense	probably damaging	1.00
R1689:Pdlim2	UTSW	14	70,408,688 (GRCm39)	missense	probably damaging	0.98
R1703:Pdlim2	UTSW	14	70,411,784 (GRCm39)	critical splice donor site	probably null
R1843:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1845:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1923:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1924:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R1925:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R2004:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R2202:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R2205:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R2237:Pdlim2	UTSW	14	70,408,698 (GRCm39)	missense	probably benign	0.05
R2843:Pdlim2	UTSW	14	70,403,549 (GRCm39)	missense	probably benign	0.02
R4042:Pdlim2	UTSW	14	70,402,228 (GRCm39)	missense	probably damaging	1.00
R4965:Pdlim2	UTSW	14	70,405,464 (GRCm39)	unclassified	probably benign
R4971:Pdlim2	UTSW	14	70,405,208 (GRCm39)	missense	probably damaging	1.00
R5951:Pdlim2	UTSW	14	70,405,229 (GRCm39)	missense	probably benign	0.06
R6252:Pdlim2	UTSW	14	70,405,137 (GRCm39)	missense	probably damaging	1.00
R7208:Pdlim2	UTSW	14	70,411,826 (GRCm39)	missense	probably damaging	1.00
R7597:Pdlim2	UTSW	14	70,403,645 (GRCm39)	missense	possibly damaging	0.58
R7627:Pdlim2	UTSW	14	70,408,924 (GRCm39)	missense	probably benign
R8342:Pdlim2	UTSW	14	70,403,563 (GRCm39)	missense	probably damaging	1.00
R8554:Pdlim2	UTSW	14	70,408,698 (GRCm39)	missense	probably benign
R9361:Pdlim2	UTSW	14	70,402,190 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGCTCTCAGTATAATCATGTCTGC -3'
(R):5'- GGGGTTGGTAAAATGAAATTCCTG -3'

Sequencing Primer
(F):5'- AATCATGTCTGCAGAGTCTGAG -3'
(R):5'- AAATTCCTGAGAGAGAGGCTTTTG -3'

Posted On

2014-08-25