Mutagenetix > Incidental Mutation

Incidental Mutation 'R1845:Pdlim2'

207678

Institutional Source

Beutler Lab

Gene Symbol

Pdlim2

Ensembl Gene

ENSMUSG00000022090

Gene Name

PDZ and LIM domain 2

Synonyms

SLIM, 4732462F18Rik, mystique

MMRRC Submission

039870-MU

Accession Numbers

Is this an essential gene?

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

Stock #

R1845 (G1)

Quality Score

178

Status

Not validated

Chromosome

Chromosomal Location

70164218-70177681 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 70164779 bp (GRCm38)

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: 97.4%
3x: 96.8%
10x: 95.0%
20x: 91.7%

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110008L16Rik	T	A	12: 55,304,332	I142N	possibly damaging	Het
1110038F14Rik	CGGG	CGGGGGG	15: 76,949,663		probably benign	Het
Abca17	A	T	17: 24,267,716	C1446S	probably damaging	Het
Asb16	C	A	11: 102,276,756	A316E	possibly damaging	Het
Axdnd1	C	T	1: 156,376,544	V384I	possibly damaging	Het
BC024139	A	T	15: 76,125,261	L207*	probably null	Het
Bcl3	T	G	7: 19,809,627	S305R	probably damaging	Het
Cachd1	T	C	4: 100,777,358	V77A	probably benign	Het
Cd101	C	T	3: 101,029,448		probably null	Het
Cela1	T	C	15: 100,685,167	N64S	probably benign	Het
Cep128	T	C	12: 91,289,598	D366G	probably benign	Het
Col12a1	A	G	9: 79,697,541	V675A	probably benign	Het
Copg1	A	G	6: 87,893,818	Y201C	probably damaging	Het
Cyp24a1	T	C	2: 170,487,917	R372G	probably benign	Het
Dcaf1	A	C	9: 106,851,962	I567L	probably benign	Het
Dcn	A	G	10: 97,506,674	D164G	probably benign	Het
Dnase2a	T	A	8: 84,909,322	H113Q	probably benign	Het
Espl1	T	C	15: 102,299,013	V304A	probably benign	Het
Fam193a	A	G	5: 34,443,372	D315G	possibly damaging	Het
Fkbp8	T	A	8: 70,531,035		probably null	Het
Foxp4	T	A	17: 47,877,959	T321S	probably null	Het
Fut10	A	G	8: 31,236,300	N361S	probably damaging	Het
Gm13762	A	G	2: 88,973,138	V251A	probably benign	Het
Gyg	A	T	3: 20,151,122	V94D	probably damaging	Het
Has2	T	C	15: 56,668,578	K247R	probably damaging	Het
Helz2	G	T	2: 181,232,085	D2205E	probably benign	Het
Hps6	T	A	19: 46,004,970	S449T	probably benign	Het
Ints10	T	C	8: 68,794,671	Y64H	probably damaging	Het
Kalrn	T	C	16: 34,356,961	H278R	probably damaging	Het
Klhdc8a	T	C	1: 132,303,810	V280A	possibly damaging	Het
Klk1b5	A	G	7: 44,220,125	M210V	probably benign	Het
Kmt2c	G	A	5: 25,373,436	A614V	probably benign	Het
Lck	T	A	4: 129,558,086	I45F	probably benign	Het
Lin7a	A	C	10: 107,412,059	E75A	probably damaging	Het
Lrp1	A	T	10: 127,578,673	C1070S	probably damaging	Het
Mapk8ip3	G	T	17: 24,914,583	N289K	probably benign	Het
Mbtps1	T	C	8: 119,522,493	D686G	probably benign	Het
Mknk1	T	A	4: 115,873,231	C178*	probably null	Het
Mtmr6	A	G	14: 60,296,735	N474S	probably damaging	Het
Mvb12b	A	G	2: 33,840,157		probably null	Het
Myh6	T	C	14: 54,944,674	K1759R	probably damaging	Het
Nfatc1	T	C	18: 80,635,531	K881E	possibly damaging	Het
Nlrp10	A	G	7: 108,927,041	F30S	probably damaging	Het
Nop14	G	T	5: 34,650,328	A430E	possibly damaging	Het
Ntn4	C	T	10: 93,707,353	R314W	probably damaging	Het
Olfr1212	A	G	2: 88,958,867	I134V	probably damaging	Het
Olfr347	A	T	2: 36,734,842	I174F	probably damaging	Het
Olfr775	A	G	10: 129,250,594	E20G	probably benign	Het
Olfr794	A	T	10: 129,571,348	Q231L	probably damaging	Het
Olfr829	A	T	9: 18,857,486	Y287F	possibly damaging	Het
Osbpl7	C	A	11: 97,059,128	S378R	probably damaging	Het
Otof	A	T	5: 30,371,723	Y1775*	probably null	Het
Parp16	T	C	9: 65,215,594	S46P	possibly damaging	Het
Pi16	A	T	17: 29,319,387	Q58L	possibly damaging	Het
Pld3	C	A	7: 27,539,452	M190I	probably benign	Het
Plscr4	T	G	9: 92,490,046	I290S	probably damaging	Het
Ppip5k2	T	C	1: 97,723,806	D928G	possibly damaging	Het
Ppp1r13l	T	A	7: 19,368,611	L15Q	probably damaging	Het
Ptpn14	C	A	1: 189,839,502	S263R	possibly damaging	Het
Sema7a	G	A	9: 57,954,899	V178I	possibly damaging	Het
Sesn2	A	T	4: 132,497,070	Y342*	probably null	Het
Shroom3	G	T	5: 92,943,086	V1151F	probably damaging	Het
Sltm	A	G	9: 70,543,032	N38S	possibly damaging	Het
Smg1	T	C	7: 118,154,622		probably benign	Het
Spsb1	A	T	4: 149,906,910	V67E	probably damaging	Het
Suox	A	G	10: 128,670,539	V540A	possibly damaging	Het
Tbc1d12	T	A	19: 38,911,085	I483N	probably damaging	Het
Tbcb	A	T	7: 30,224,499	D198E	possibly damaging	Het
Tbce	T	C	13: 14,019,709	K122E	probably benign	Het
Tcap	T	A	11: 98,384,379	L113H	probably damaging	Het
Thsd7a	A	T	6: 12,321,041	I1545N	probably damaging	Het
Tmed10	T	C	12: 85,374,503	T55A	possibly damaging	Het
Tmem268	T	A	4: 63,579,943	V200D	probably damaging	Het
Tmem45b	A	C	9: 31,431,355	I50M	probably damaging	Het
Trp53bp2	T	C	1: 182,458,903	W1103R	probably damaging	Het
Ttn	C	T	2: 76,764,033	V20524M	probably damaging	Het
Ulk2	A	T	11: 61,812,738	N379K	probably benign	Het
Vmn1r59	A	G	7: 5,454,554	V69A	probably benign	Het
Vmn2r10	A	T	5: 109,001,995	Y394*	probably null	Het
Zfp212	T	C	6: 47,931,541	S485P	probably benign	Het
Zfp512b	A	T	2: 181,585,735	C776S	probably damaging	Het
Zfp518b	A	G	5: 38,671,741	Y974H	probably damaging	Het

Other mutations in Pdlim2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02295:Pdlim2	APN	14	70166083	splice site	probably benign
IGL02338:Pdlim2	APN	14	70174457	missense	probably damaging	1.00
IGL03286:Pdlim2	APN	14	70174476	missense	possibly damaging	0.88
PIT4504001:Pdlim2	UTSW	14	70166130	missense	probably benign	0.44
R0751:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R0768:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R0832:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R1167:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R1207:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R1207:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R1343:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R1412:Pdlim2	UTSW	14	70174324	splice site	probably benign
R1595:Pdlim2	UTSW	14	70164744	missense	probably damaging	1.00
R1689:Pdlim2	UTSW	14	70171239	missense	probably damaging	0.98
R1703:Pdlim2	UTSW	14	70174335	critical splice donor site	probably null
R1843:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R1923:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R1924:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R1925:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R2004:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R2005:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R2202:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R2205:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R2237:Pdlim2	UTSW	14	70171249	missense	probably benign	0.05
R2843:Pdlim2	UTSW	14	70166100	missense	probably benign	0.02
R4042:Pdlim2	UTSW	14	70164779	missense	probably damaging	1.00
R4965:Pdlim2	UTSW	14	70168015	unclassified	probably benign
R4971:Pdlim2	UTSW	14	70167759	missense	probably damaging	1.00
R5951:Pdlim2	UTSW	14	70167780	missense	probably benign	0.06
R6252:Pdlim2	UTSW	14	70167688	missense	probably damaging	1.00
R7208:Pdlim2	UTSW	14	70174377	missense	probably damaging	1.00
R7597:Pdlim2	UTSW	14	70166196	missense	possibly damaging	0.58
R7627:Pdlim2	UTSW	14	70171475	missense	probably benign
R8342:Pdlim2	UTSW	14	70166114	missense	probably damaging	1.00
R8554:Pdlim2	UTSW	14	70171249	missense	probably benign
R9361:Pdlim2	UTSW	14	70164741	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCTCTCAGTATAATCATGTCTGCAG -3'
(R):5'- TGGGGTTGGTAAAATGAAATTCCTG -3'

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

Posted On

2014-06-23