Mutagenetix > Incidental Mutation

Incidental Mutation 'R5969:Pdlim4'

470753

Institutional Source

Beutler Lab

Gene Symbol

Pdlim4

Ensembl Gene

ENSMUSG00000020388

Gene Name

PDZ and LIM domain 4

Synonyms

Ril

MMRRC Submission

044152-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.236) question?

Stock #

R5969 (G1)

Quality Score

191

Status

Validated

Chromosome

Chromosomal Location

53945754-53959840 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 53954482 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Arginine at position 75 (H75R)

Ref Sequence

ENSEMBL: ENSMUSP00000090797 (fasta)

Gene Model

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

AlphaFold

P70271

Predicted Effect

probably benign
Transcript: ENSMUST00000018755
AA Change: H75R

PolyPhen 2 Score 0.235 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000018755
Gene: ENSMUSG00000020388
AA Change: H75R

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: H75R

PolyPhen 2 Score 0.504 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000090797
Gene: ENSMUSG00000020388
AA Change: H75R

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127271

Predicted Effect

probably benign
Transcript: ENSMUST00000144477
AA Change: H16R

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000121248
Gene: ENSMUSG00000020388
AA Change: H16R

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151948

Meta Mutation Damage Score

0.0856

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.2%

Validation Efficiency

99% (67/68)

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aaas	A	C	15: 102,258,999 (GRCm39)	Y19D	probably damaging	Het
Abca13	T	A	11: 9,242,214 (GRCm39)	L1359*	probably null	Het
Ahi1	A	T	10: 20,860,292 (GRCm39)	D671V	probably damaging	Het
Ahnak	T	C	19: 8,993,949 (GRCm39)	S5078P	probably damaging	Het
Ankhd1	A	T	18: 36,733,887 (GRCm39)	T584S	probably damaging	Het
Apba2	T	A	7: 64,394,195 (GRCm39)	L568*	probably null	Het
Cenpn	C	A	8: 117,667,276 (GRCm39)	L300I	probably damaging	Het
Cmya5	A	T	13: 93,226,052 (GRCm39)	L3012Q	possibly damaging	Het
Cnnm1	T	C	19: 43,479,911 (GRCm39)	S819P	probably damaging	Het
Cpa6	A	T	1: 10,559,108 (GRCm39)	S87T	probably benign	Het
Crybg2	T	A	4: 133,803,003 (GRCm39)		probably null	Het
Csmd1	T	A	8: 16,121,367 (GRCm39)	T1777S	probably benign	Het
Csmd3	G	T	15: 47,811,386 (GRCm39)	P1235Q	probably damaging	Het
Cxcr4	T	A	1: 128,517,584 (GRCm39)	N24Y	probably benign	Het
D630003M21Rik	G	T	2: 158,059,628 (GRCm39)	H91N	probably damaging	Het
Ece1	T	C	4: 137,689,051 (GRCm39)		probably null	Het
Edc3	T	C	9: 57,620,711 (GRCm39)	S11P	probably damaging	Het
Eif1ad14	T	C	12: 87,886,248 (GRCm39)	D127G	unknown	Het
Exoc3	G	A	13: 74,320,305 (GRCm39)	Q719*	probably null	Het
Fam13a	A	G	6: 58,942,183 (GRCm39)	M203T	probably damaging	Het
Fchsd1	C	T	18: 38,092,926 (GRCm39)		probably benign	Het
Fhip2a	C	T	19: 57,372,555 (GRCm39)	R602*	probably null	Het
Fxyd2	T	A	9: 45,319,628 (GRCm39)	I30N	probably damaging	Het
Gapt	A	G	13: 110,490,480 (GRCm39)	V61A	probably benign	Het
Glb1l2	C	T	9: 26,692,038 (GRCm39)	A74T	probably damaging	Het
Gpr35	T	C	1: 92,910,942 (GRCm39)	V2A	probably damaging	Het
Gtf3c1	A	G	7: 125,244,848 (GRCm39)	S1729P	possibly damaging	Het
Heatr5a	T	C	12: 52,005,823 (GRCm39)	T51A	probably benign	Het
Kat6b	G	A	14: 21,720,860 (GRCm39)	M1737I	probably damaging	Het
Kif20a	G	A	18: 34,765,468 (GRCm39)	A822T	probably benign	Het
Klk10	A	G	7: 43,434,409 (GRCm39)	Y267C	probably damaging	Het
Lgmn	T	C	12: 102,372,086 (GRCm39)	Y98C	probably damaging	Het
Lyst	A	C	13: 13,862,398 (GRCm39)		probably null	Het
Man2a1	A	G	17: 64,932,375 (GRCm39)	K154R	probably benign	Het
Mfng	A	T	15: 78,648,582 (GRCm39)	V165D	possibly damaging	Het
Mto1	A	G	9: 78,360,187 (GRCm39)	E225G	probably damaging	Het
Notch3	C	A	17: 32,372,858 (GRCm39)	C571F	probably damaging	Het
Nup205	C	T	6: 35,154,513 (GRCm39)		probably benign	Het
Or51b6	T	A	7: 103,556,117 (GRCm39)	I157N	probably damaging	Het
P2ry14	T	A	3: 59,022,579 (GRCm39)	I303F	probably damaging	Het
Pcnx3	T	C	19: 5,735,563 (GRCm39)	D421G	probably damaging	Het
Phf21a	A	T	2: 92,051,956 (GRCm39)	H17L	probably damaging	Het
Ppid	T	A	3: 79,505,024 (GRCm39)	N122K	probably damaging	Het
Ppp4r3a	T	C	12: 101,009,838 (GRCm39)	I613V	probably benign	Het
Prcp	C	T	7: 92,566,974 (GRCm39)	P229S	probably benign	Het
Ralgds	T	C	2: 28,432,426 (GRCm39)	V85A	probably damaging	Het
Rgs22	G	A	15: 36,015,782 (GRCm39)	T1034I	probably benign	Het
Slc4a3	T	C	1: 75,526,623 (GRCm39)	V48A	probably damaging	Het
Snx16	A	T	3: 10,503,217 (GRCm39)	M10K	possibly damaging	Het
Svep1	G	A	4: 58,070,977 (GRCm39)	Q2270*	probably null	Het
Tmem185b	T	G	1: 119,455,193 (GRCm39)	I318S	probably benign	Het
Tnik	C	T	3: 28,675,097 (GRCm39)	R657C	probably damaging	Het
Top3b	T	C	16: 16,701,429 (GRCm39)		probably null	Het
Trim40	C	T	17: 37,193,319 (GRCm39)	R203H	probably benign	Het
Triobp	T	A	15: 78,851,740 (GRCm39)	N631K	probably benign	Het
Ubr3	T	G	2: 69,809,730 (GRCm39)	Y1233*	probably null	Het
Vgll3	A	G	16: 65,636,449 (GRCm39)	D200G	probably damaging	Het
Vmn2r24	G	A	6: 123,755,981 (GRCm39)	E18K	probably benign	Het
Zfp141	C	A	7: 42,138,912 (GRCm39)	R40L	probably damaging	Het

Other mutations in Pdlim4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01377:Pdlim4	APN	11	53,947,130 (GRCm39)	missense	probably benign	0.43
IGL02005:Pdlim4	APN	11	53,950,810 (GRCm39)	missense	probably benign	0.10
IGL02305:Pdlim4	APN	11	53,946,759 (GRCm39)	missense	probably damaging	1.00
IGL03073:Pdlim4	APN	11	53,954,467 (GRCm39)	missense	probably damaging	1.00
BB001:Pdlim4	UTSW	11	53,946,048 (GRCm39)	nonsense	probably null
BB011:Pdlim4	UTSW	11	53,946,048 (GRCm39)	nonsense	probably null
R0008:Pdlim4	UTSW	11	53,945,875 (GRCm39)	missense	probably damaging	1.00
R0612:Pdlim4	UTSW	11	53,959,713 (GRCm39)	missense	probably damaging	1.00
R1646:Pdlim4	UTSW	11	53,947,080 (GRCm39)	missense	possibly damaging	0.94
R1754:Pdlim4	UTSW	11	53,946,699 (GRCm39)	missense	possibly damaging	0.82
R2132:Pdlim4	UTSW	11	53,954,563 (GRCm39)	missense	possibly damaging	0.70
R3037:Pdlim4	UTSW	11	53,947,083 (GRCm39)	missense	probably benign	0.15
R4210:Pdlim4	UTSW	11	53,946,744 (GRCm39)	missense	possibly damaging	0.70
R5787:Pdlim4	UTSW	11	53,946,042 (GRCm39)	missense	probably damaging	1.00
R6862:Pdlim4	UTSW	11	53,946,674 (GRCm39)	missense	probably damaging	1.00
R7924:Pdlim4	UTSW	11	53,946,048 (GRCm39)	nonsense	probably null
R8927:Pdlim4	UTSW	11	53,950,790 (GRCm39)	missense	probably benign	0.01
R8928:Pdlim4	UTSW	11	53,950,790 (GRCm39)	missense	probably benign	0.01
R9023:Pdlim4	UTSW	11	53,959,662 (GRCm39)	unclassified	probably benign
R9026:Pdlim4	UTSW	11	53,946,280 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CAAACCCTGGATTGTAAAGGC -3'
(R):5'- TTGATGGGAATCTAGTGCAGGC -3'

Sequencing Primer
(F):5'- TGGATTGTAAAGGCTCCTCCCAG -3'
(R):5'- TGCAGGCGTCCATGTAGTAAC -3'

Posted On

2017-03-31