Mutagenetix > Incidental Mutations

Incidental Mutation 'R8927:Pdlim4'

690166

Institutional Source

Beutler Lab

Gene Symbol

Pdlim4

Ensembl Gene

ENSMUSG00000020388

Gene Name

PDZ and LIM domain 4

Synonyms

Ril

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.250) question?

Stock #

R8927 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

54054928-54069014 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 54059964 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 100 (R100G)

Ref Sequence

ENSEMBL: ENSMUSP00000018755 (fasta)

Gene Model

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

AlphaFold

P70271

Predicted Effect

probably benign
Transcript: ENSMUST00000018755
AA Change: R100G

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000018755
Gene: ENSMUSG00000020388
AA Change: R100G

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: R100G

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000090797
Gene: ENSMUSG00000020388
AA Change: R100G

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

Predicted Effect

probably benign
Transcript: ENSMUST00000144477
AA Change: R41G

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000121248
Gene: ENSMUSG00000020388
AA Change: R41G

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: 98.9%

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700022I11Rik	A	T	4: 42,972,251	Y528F	probably benign	Het
A630089N07Rik	A	T	16: 98,066,167	H198Q	probably damaging	Het
Abcb9	T	C	5: 124,083,643	T223A	probably benign	Het
Actc1	T	A	2: 114,050,400	K115*	probably null	Het
Angptl2	G	A	2: 33,242,304	D308N	probably benign	Het
Arl4d	A	C	11: 101,667,066	Q139H	possibly damaging	Het
Aspm	T	A	1: 139,490,387	C2951*	probably null	Het
Atp23	A	T	10: 126,887,493	*247R	probably null	Het
B3gnt7	T	A	1: 86,305,117	S28R	probably benign	Het
Bmp7	C	T	2: 172,879,418	R288H	probably damaging	Het
Bsdc1	G	T	4: 129,461,646		probably benign	Het
C130060K24Rik	C	A	6: 65,381,613	S107*	probably null	Het
Ccdc146	T	C	5: 21,333,062	E88G	probably damaging	Het
Ccdc73	C	A	2: 104,992,197	D2E		Het
Cdc5l	C	A	17: 45,410,913	R477L		Het
Cdh22	T	A	2: 165,123,584	H529L	possibly damaging	Het
Chchd3	T	A	6: 32,804,016	E178D	probably benign	Het
Ciz1	A	T	2: 32,367,500	R186*	probably null	Het
Copa	T	A	1: 172,104,170	H329Q	probably null	Het
Dcaf7	A	G	11: 106,051,926	D233G	probably damaging	Het
Dclk2	G	T	3: 86,831,741	P317Q	probably damaging	Het
Dsc3	A	T	18: 19,974,177	H462Q	probably benign	Het
Fn1	T	C	1: 71,599,376	N1998S	probably benign	Het
Fpr2	T	C	17: 17,893,462	L240S	possibly damaging	Het
Fzd9	A	T	5: 135,249,735	M432K	probably damaging	Het
Gm14025	A	G	2: 129,040,869	S76P		Het
Gm15922	A	C	7: 3,739,359	N56K	probably benign	Het
Gm37596	T	A	3: 93,692,643	T140S	probably benign	Het
Gm5862	T	A	5: 26,021,680	I75F	probably damaging	Het
Gpr45	T	A	1: 43,033,154	V319D	probably damaging	Het
Hist1h4j	T	C	13: 21,735,355	V87A	possibly damaging	Het
Igfn1	T	A	1: 135,978,246	R275W	probably damaging	Het
Inafm1	G	A	7: 16,273,055	A79V	unknown	Het
Itfg1	C	T	8: 85,840,791		probably benign	Het
Klhl35	T	G	7: 99,471,014	I366S	probably damaging	Het
Lysmd1	A	T	3: 95,138,520	I223F	probably damaging	Het
Mrps30	A	G	13: 118,386,669	L189P	probably damaging	Het
Ms4a4d	A	C	19: 11,556,210	T152P	probably benign	Het
Mtcl1	A	T	17: 66,448,633	I238K	probably benign	Het
Musk	T	C	4: 58,301,638	I132T	probably damaging	Het
Myh2	A	T	11: 67,188,683	M989L	probably benign	Het
Myh8	G	A	11: 67,283,255	R172H	probably benign	Het
Nt5c1a	C	T	4: 123,208,488	T69M	possibly damaging	Het
Nuak2	T	A	1: 132,328,178	D196E	probably damaging	Het
Olfr1020	A	T	2: 85,849,574	I41F	possibly damaging	Het
Olfr1055	T	C	2: 86,347,746	T7A	possibly damaging	Het
Olfr1086	T	C	2: 86,677,286	T16A	probably benign	Het
Olfr652	A	T	7: 104,565,022	H267L	probably damaging	Het
Palb2	A	T	7: 122,124,598	C643S	probably damaging	Het
Pde5a	T	A	3: 122,839,600	I706N	probably damaging	Het
Pip5k1c	T	A	10: 81,293,072	V5E	possibly damaging	Het
Plekhm1	A	G	11: 103,377,213	V644A	probably benign	Het
Plk2	T	G	13: 110,399,216	V524G	probably damaging	Het
Ppl	T	A	16: 5,087,610	N1607I	probably benign	Het
Prag1	T	G	8: 36,147,206	V1304G	probably damaging	Het
Prex1	C	T	2: 166,585,075	V1077M	probably damaging	Het
Prmt6	T	C	3: 110,250,932	S14G	probably benign	Het
Psrc1	T	G	3: 108,386,657	S263R	probably damaging	Het
Rbp7	A	T	4: 149,453,501	L36*	probably null	Het
Rgs12	G	T	5: 34,966,289	W472L	possibly damaging	Het
Rrp8	C	A	7: 105,734,866	C143F	possibly damaging	Het
Sart1	T	C	19: 5,388,501	S43G	probably benign	Het
Setx	A	G	2: 29,126,959	T25A	possibly damaging	Het
Skint5	G	A	4: 113,483,902	T1414I	probably benign	Het
Sorbs2	T	A	8: 45,795,915	S734R	probably damaging	Het
Spon1	T	C	7: 114,030,357		probably null	Het
Sptbn1	C	T	11: 30,138,962	V767I	probably damaging	Het
Srf	T	C	17: 46,549,169	I477V	probably damaging	Het
Tanc2	A	G	11: 105,810,505	Y282C	probably damaging	Het
Tbc1d23	A	G	16: 57,171,789	Y603H	probably damaging	Het
Tfap4	T	C	16: 4,551,354	D134G	probably damaging	Het
Tmem200c	A	G	17: 68,841,738	T439A	probably benign	Het
Tmem63b	A	T	17: 45,664,982	M515K	probably damaging	Het
Tnc	A	T	4: 64,007,358	N980K	probably damaging	Het
Ttc23l	T	A	15: 10,530,634	L297F	probably damaging	Het
Vmn1r170	A	G	7: 23,606,389	N72S	possibly damaging	Het
Vmn2r8	T	C	5: 108,802,265	M239V		Het
Vopp1	A	G	6: 57,754,593	F138L	probably damaging	Het
Vps41	T	A	13: 18,745,331	F79I	probably benign	Het
Zfp317	T	C	9: 19,641,225	M1T	probably null	Het

Other mutations in Pdlim4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01377:Pdlim4	APN	11	54056304	missense	probably benign	0.43
IGL02005:Pdlim4	APN	11	54059984	missense	probably benign	0.10
IGL02305:Pdlim4	APN	11	54055933	missense	probably damaging	1.00
IGL03073:Pdlim4	APN	11	54063641	missense	probably damaging	1.00
BB001:Pdlim4	UTSW	11	54055222	nonsense	probably null
BB011:Pdlim4	UTSW	11	54055222	nonsense	probably null
R0008:Pdlim4	UTSW	11	54055049	missense	probably damaging	1.00
R0612:Pdlim4	UTSW	11	54068887	missense	probably damaging	1.00
R1646:Pdlim4	UTSW	11	54056254	missense	possibly damaging	0.94
R1754:Pdlim4	UTSW	11	54055873	missense	possibly damaging	0.82
R2132:Pdlim4	UTSW	11	54063737	missense	possibly damaging	0.70
R3037:Pdlim4	UTSW	11	54056257	missense	probably benign	0.15
R4210:Pdlim4	UTSW	11	54055918	missense	possibly damaging	0.70
R5787:Pdlim4	UTSW	11	54055216	missense	probably damaging	1.00
R5969:Pdlim4	UTSW	11	54063656	missense	possibly damaging	0.50
R6862:Pdlim4	UTSW	11	54055848	missense	probably damaging	1.00
R7924:Pdlim4	UTSW	11	54055222	nonsense	probably null
R8928:Pdlim4	UTSW	11	54059964	missense	probably benign	0.01
R9026:Pdlim4	UTSW	11	54055454	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- AAGCAGGCATGTCCTAGAGG -3'
(R):5'- CTCCTGCAAGGTCTTTAGGAATG -3'

Sequencing Primer
(F):5'- GAGGAGCTGTCTACTTCAGTATACC -3'
(R):5'- CTGCAAGGTCTTTAGGAATGAGACC -3'

Posted On

2021-11-19