Mutagenetix > Incidental Mutation

Incidental Mutation 'BB001:Pdlim4'

642114

Institutional Source

Beutler Lab

Gene Symbol

Pdlim4

Ensembl Gene

ENSMUSG00000020388

Gene Name

PDZ and LIM domain 4

Synonyms

Ril

Accession Numbers

Essential gene?

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

Stock #

BB001

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

54054928-54069014 bp(-) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to A at 54055222 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Stop codon at position 230 (R230*)

Ref Sequence

ENSEMBL: ENSMUSP00000090797 (fasta)

Gene Model

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

AlphaFold

P70271

Predicted Effect

probably damaging
Transcript: ENSMUST00000018755
AA Change: A269V

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000018755
Gene: ENSMUSG00000020388
AA Change: A269V

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

probably null
Transcript: ENSMUST00000093109
AA Change: R230*

SMART Domains

Protein: ENSMUSP00000090797
Gene: ENSMUSG00000020388
AA Change: R230*

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

Predicted Effect

probably benign
Transcript: ENSMUST00000144477

SMART Domains

Protein: ENSMUSP00000121248
Gene: ENSMUSG00000020388

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acacb	A	G	5: 114,245,220 (GRCm38)	K2155E	possibly damaging	Het
Adgre5	G	A	8: 83,729,400 (GRCm38)	P256S	possibly damaging	Het
Adipor1	T	A	1: 134,425,993 (GRCm38)	V172D	probably damaging	Het
Ahsa1	T	C	12: 87,270,456 (GRCm38)		probably null	Het
Ankrd11	T	C	8: 122,895,902 (GRCm38)	I404V	possibly damaging	Het
Asxl3	G	A	18: 22,525,545 (GRCm38)	R2204Q	probably damaging	Het
Barhl2	A	G	5: 106,457,649 (GRCm38)	S65P	unknown	Het
Bbx	A	T	16: 50,224,308 (GRCm38)	L630H	probably damaging	Het
Cars1	T	C	7: 143,569,871 (GRCm38)	T531A	possibly damaging	Het
Catsperb	T	A	12: 101,520,565 (GRCm38)	H450Q	probably benign	Het
Cdt1	T	C	8: 122,569,352 (GRCm38)	L135P	probably damaging	Het
Cfap206	T	A	4: 34,728,833 (GRCm38)	H24L	probably benign	Het
Cilk1	T	C	9: 78,155,464 (GRCm38)	L260P	probably damaging	Het
Cnga4	T	A	7: 105,407,821 (GRCm38)	V480E	probably benign	Het
Cnot1	ACG	A	8: 95,745,647 (GRCm38)		probably null	Het
Ctcfl	G	A	2: 173,113,656 (GRCm38)	T271I	possibly damaging	Het
Dlc1	T	C	8: 36,571,416 (GRCm38)	R1003G	probably benign	Het
Dnah7b	A	G	1: 46,219,430 (GRCm38)	D1927G	probably benign	Het
Dscc1	A	T	15: 55,082,176 (GRCm38)	D374E	probably benign	Het
Eci2	G	A	13: 34,993,070 (GRCm38)	Q69*	probably null	Het
Ep300	C	A	15: 81,649,502 (GRCm38)	P1920Q	unknown	Het
Epha5	A	G	5: 84,084,846 (GRCm38)	Y629H	possibly damaging	Het
Fat2	G	A	11: 55,262,787 (GRCm38)	T3533I	probably benign	Het
Fat3	T	C	9: 15,999,297 (GRCm38)	N1803S	probably damaging	Het
Fcrl2	T	C	3: 87,259,533 (GRCm38)	Y51C	probably damaging	Het
G530012D18Rik	C	G	1: 85,577,214 (GRCm38)	D113E	unknown	Het
Gcnt2	A	T	13: 40,918,564 (GRCm38)	K228*	probably null	Het
Gucy2c	A	T	6: 136,763,055 (GRCm38)	V258E	probably benign	Het
Hecw1	C	A	13: 14,322,528 (GRCm38)	L298F	probably damaging	Het
Hydin	T	G	8: 110,418,471 (GRCm38)	V818G	possibly damaging	Het
Hykk	A	G	9: 54,922,240 (GRCm38)	Y131C	probably damaging	Het
Mpo	A	G	11: 87,794,840 (GRCm38)	D48G	probably damaging	Het
Mrps10	T	C	17: 47,378,283 (GRCm38)	*202Q	probably null	Het
Mrps14	T	C	1: 160,196,989 (GRCm38)	V30A	probably benign	Het
Mtmr7	G	A	8: 40,606,884 (GRCm38)	A62V	possibly damaging	Het
Muc2	G	T	7: 141,695,388 (GRCm38)	G497W	probably damaging	Het
Nnt	A	T	13: 119,386,645 (GRCm38)	V237D	probably damaging	Het
Nox4	G	T	7: 87,374,381 (GRCm38)	V492L	probably benign	Het
Obscn	C	G	11: 59,112,555 (GRCm38)	E1306Q	probably benign	Het
Or5ak23	T	C	2: 85,414,219 (GRCm38)	Y220C	probably benign	Het
Or6aa1	A	G	7: 86,394,730 (GRCm38)	I256T	probably damaging	Het
Pard3	A	G	8: 127,410,750 (GRCm38)	N861S	probably benign	Het
Pinlyp	C	T	7: 24,542,125 (GRCm38)	V159M	possibly damaging	Het
Pla2g4d	T	C	2: 120,289,164 (GRCm38)		probably benign	Het
Plcb1	A	T	2: 135,359,693 (GRCm38)	T855S	probably benign	Het
Pot1a	T	A	6: 25,753,310 (GRCm38)	D409V	possibly damaging	Het
Prom1	T	C	5: 44,029,769 (GRCm38)	D382G	probably benign	Het
Prss16	A	T	13: 22,008,664 (GRCm38)	N83K	probably damaging	Het
Ptprn2	A	G	12: 116,841,264 (GRCm38)	D133G	probably benign	Het
Rasef	C	T	4: 73,740,929 (GRCm38)		probably null	Het
Rbak	A	G	5: 143,174,486 (GRCm38)	S271P	probably damaging	Het
Rbm20	A	T	19: 53,677,585 (GRCm38)	I60F	possibly damaging	Het
Rftn1	G	T	17: 50,047,380 (GRCm38)	A318D	probably damaging	Het
Serpinb3c	A	G	1: 107,273,174 (GRCm38)	L171P	probably damaging	Het
Slc25a19	T	C	11: 115,615,550 (GRCm38)	Y211C	unknown	Het
Sorbs2	C	T	8: 45,795,470 (GRCm38)	S586L	probably damaging	Het
Spesp1	A	T	9: 62,273,451 (GRCm38)	S58R	probably benign	Het
Spryd3	A	G	15: 102,118,327 (GRCm38)	I329T	probably benign	Het
St8sia2	G	A	7: 73,966,952 (GRCm38)	L113F	probably damaging	Het
Star	T	C	8: 25,809,855 (GRCm38)	I75T	possibly damaging	Het
Tasor2	A	T	13: 3,594,331 (GRCm38)	F129Y	possibly damaging	Het
Tdrd6	T	A	17: 43,627,806 (GRCm38)	I784F	possibly damaging	Het
Tex55	G	A	16: 38,812,464 (GRCm38)	Q369*	probably null	Het
Tsc22d4	A	G	5: 137,768,011 (GRCm38)	I144V	unknown	Het
Tspan8	T	C	10: 115,833,324 (GRCm38)		probably null	Het
Ttll9	C	T	2: 152,962,487 (GRCm38)		probably benign	Het
Ubr4	T	G	4: 139,467,276 (GRCm38)	L1160R	unknown	Het
Ufd1	A	G	16: 18,823,285 (GRCm38)	Y162C	possibly damaging	Het
Unc13c	A	T	9: 73,734,408 (GRCm38)	F1268I	probably benign	Het
Uvssa	T	C	5: 33,410,951 (GRCm38)	I561T	probably damaging	Het
Vmn2r15	A	T	5: 109,286,388 (GRCm38)	S817T	probably damaging	Het
Ybx1	T	C	4: 119,282,279 (GRCm38)	E173G	probably damaging	Het
Zc3h6	T	C	2: 129,015,480 (GRCm38)	S640P	possibly damaging	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
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
R1646:Pdlim4	UTSW	11	54,056,254 (GRCm38)	missense	possibly damaging	0.94
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'- GCATTGGGGTATACAGCCAC -3'
(R):5'- ACCTGCCCTCTGGATTTCAG -3'

Sequencing Primer
(F):5'- TGGGGTATACAGCCACCACATC -3'
(R):5'- TCGGTGCTCCACTGAGTG -3'

Posted On

2020-08-01