Mutagenetix > Incidental Mutation

Incidental Mutation 'R9670:Prg4'

727989

Institutional Source

Beutler Lab

Gene Symbol

Prg4

Ensembl Gene

ENSMUSG00000006014

Gene Name

proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)

Synonyms

MSF, SZP, lubricin, DOL54

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.125) question?

Stock #

R9670 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

150325163-150341916 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 150326618 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 357 (K357R)

Ref Sequence

ENSEMBL: ENSMUSP00000006171 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006171] [ENSMUST00000111901] [ENSMUST00000111902] [ENSMUST00000119161] [ENSMUST00000124484] [ENSMUST00000124973] [ENSMUST00000161611] [ENSMUST00000162367] [ENSMUST00000164600]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000006171
AA Change: K357R

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000006171
Gene: ENSMUSG00000006014
AA Change: K357R

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
SO	26	68	9.21e-18	SMART
SO	69	108	4.21e-12	SMART
low complexity region	110	124	N/A	INTRINSIC
HX	169	211	1.67e-7	SMART
HX	213	256	3.76e-10	SMART
Blast:HX	369	422	2e-27	BLAST

Predicted Effect

unknown
Transcript: ENSMUST00000111901
AA Change: K899R

SMART Domains

Protein: ENSMUSP00000107532
Gene: ENSMUSG00000006014
AA Change: K899R

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
SO	26	68	9.21e-18	SMART
SO	69	108	4.21e-12	SMART
low complexity region	110	124	N/A	INTRINSIC
low complexity region	141	151	N/A	INTRINSIC
low complexity region	189	221	N/A	INTRINSIC
low complexity region	241	535	N/A	INTRINSIC
low complexity region	570	623	N/A	INTRINSIC
HX	711	753	1.67e-7	SMART
HX	755	798	3.76e-10	SMART
Blast:HX	911	964	5e-27	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000111902
AA Change: K946R

PolyPhen 2 Score 0.175 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000107533
Gene: ENSMUSG00000006014
AA Change: K946R

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
SO	25	67	2.71e-15	SMART
low complexity region	69	81	N/A	INTRINSIC
low complexity region	86	143	N/A	INTRINSIC
low complexity region	150	171	N/A	INTRINSIC
low complexity region	188	198	N/A	INTRINSIC
low complexity region	236	268	N/A	INTRINSIC
low complexity region	288	582	N/A	INTRINSIC
internal_repeat_1	588	614	2.72e-5	PROSPERO
low complexity region	617	670	N/A	INTRINSIC
internal_repeat_1	680	706	2.72e-5	PROSPERO
HX	758	800	1.67e-7	SMART
HX	802	845	3.76e-10	SMART
Blast:HX	958	1011	4e-27	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000119161

SMART Domains

Protein: ENSMUSP00000112606
Gene: ENSMUSG00000006005

Domain	Start	End	E-Value	Type
coiled coil region	49	370	N/A	INTRINSIC
coiled coil region	423	515	N/A	INTRINSIC
low complexity region	518	534	N/A	INTRINSIC
coiled coil region	539	604	N/A	INTRINSIC
low complexity region	690	703	N/A	INTRINSIC
low complexity region	782	795	N/A	INTRINSIC
low complexity region	811	826	N/A	INTRINSIC
low complexity region	1003	1019	N/A	INTRINSIC
Pfam:TPR_MLP1_2	1036	1167	9.1e-33	PFAM
coiled coil region	1215	1421	N/A	INTRINSIC
coiled coil region	1473	1629	N/A	INTRINSIC
internal_repeat_3	1630	1691	1.48e-5	PROSPERO
low complexity region	1695	1717	N/A	INTRINSIC
low complexity region	1761	1777	N/A	INTRINSIC
internal_repeat_5	1814	1827	5.58e-5	PROSPERO
internal_repeat_3	1819	1881	1.48e-5	PROSPERO
internal_repeat_4	1875	1895	5.58e-5	PROSPERO
internal_repeat_1	1893	1919	2.03e-6	PROSPERO
low complexity region	1920	1933	N/A	INTRINSIC
low complexity region	1942	1981	N/A	INTRINSIC
low complexity region	1989	2014	N/A	INTRINSIC
internal_repeat_4	2017	2036	5.58e-5	PROSPERO
low complexity region	2059	2078	N/A	INTRINSIC
internal_repeat_2	2084	2135	3.95e-6	PROSPERO
internal_repeat_5	2127	2140	5.58e-5	PROSPERO
internal_repeat_1	2154	2179	2.03e-6	PROSPERO
internal_repeat_2	2156	2212	3.95e-6	PROSPERO
low complexity region	2239	2251	N/A	INTRINSIC
low complexity region	2263	2277	N/A	INTRINSIC
low complexity region	2292	2314	N/A	INTRINSIC
low complexity region	2346	2357	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000124484

SMART Domains

Protein: ENSMUSP00000121991
Gene: ENSMUSG00000006005

Domain	Start	End	E-Value	Type
low complexity region	26	38	N/A	INTRINSIC
low complexity region	50	64	N/A	INTRINSIC
low complexity region	79	101	N/A	INTRINSIC
low complexity region	133	144	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000124973

SMART Domains

Protein: ENSMUSP00000117616
Gene: ENSMUSG00000006005

Domain	Start	End	E-Value	Type
low complexity region	3	14	N/A	INTRINSIC
low complexity region	24	77	N/A	INTRINSIC
coiled coil region	123	444	N/A	INTRINSIC
coiled coil region	497	589	N/A	INTRINSIC
low complexity region	592	608	N/A	INTRINSIC
coiled coil region	613	678	N/A	INTRINSIC
low complexity region	764	777	N/A	INTRINSIC
low complexity region	856	869	N/A	INTRINSIC
low complexity region	885	900	N/A	INTRINSIC
low complexity region	1077	1093	N/A	INTRINSIC
Pfam:TPR_MLP1_2	1112	1240	5.1e-37	PFAM
coiled coil region	1289	1495	N/A	INTRINSIC
low complexity region	1682	1698	N/A	INTRINSIC
internal_repeat_5	1703	1750	8.04e-5	PROSPERO
internal_repeat_3	1704	1765	1.07e-5	PROSPERO
low complexity region	1769	1791	N/A	INTRINSIC
low complexity region	1835	1851	N/A	INTRINSIC
internal_repeat_5	1857	1900	8.04e-5	PROSPERO
internal_repeat_6	1887	1911	8.04e-5	PROSPERO
internal_repeat_3	1893	1955	1.07e-5	PROSPERO
internal_repeat_4	1949	1969	4.1e-5	PROSPERO
internal_repeat_1	1967	1993	1.42e-6	PROSPERO
low complexity region	1994	2007	N/A	INTRINSIC
low complexity region	2016	2055	N/A	INTRINSIC
low complexity region	2063	2088	N/A	INTRINSIC
internal_repeat_4	2091	2110	4.1e-5	PROSPERO
internal_repeat_6	2108	2132	8.04e-5	PROSPERO
low complexity region	2133	2152	N/A	INTRINSIC
internal_repeat_2	2158	2209	2.78e-6	PROSPERO
internal_repeat_1	2228	2253	1.42e-6	PROSPERO
internal_repeat_2	2230	2286	2.78e-6	PROSPERO
low complexity region	2313	2325	N/A	INTRINSIC
low complexity region	2337	2351	N/A	INTRINSIC
low complexity region	2366	2388	N/A	INTRINSIC
low complexity region	2420	2431	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000161611
AA Change: K1155R

SMART Domains

Protein: ENSMUSP00000125677
Gene: ENSMUSG00000006014
AA Change: K1155R

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
SO	26	68	9.21e-18	SMART
SO	69	108	2.77e-12	SMART
low complexity region	110	122	N/A	INTRINSIC
low complexity region	127	184	N/A	INTRINSIC
low complexity region	191	212	N/A	INTRINSIC
low complexity region	229	239	N/A	INTRINSIC
internal_repeat_3	244	271	7.42e-5	PROSPERO
low complexity region	277	309	N/A	INTRINSIC
Pfam:Cornifin	578	691	2.2e-9	PFAM
internal_repeat_3	796	825	7.42e-5	PROSPERO
internal_repeat_2	797	823	1.24e-5	PROSPERO
low complexity region	826	879	N/A	INTRINSIC
internal_repeat_2	889	915	1.24e-5	PROSPERO
HX	967	1009	1.67e-7	SMART
HX	1011	1054	3.76e-10	SMART
Blast:HX	1167	1220	6e-27	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000162367
AA Change: K357R

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000125551
Gene: ENSMUSG00000006014
AA Change: K357R

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
SO	26	68	9.21e-18	SMART
SO	69	108	4.21e-12	SMART
low complexity region	110	124	N/A	INTRINSIC
HX	169	211	1.67e-7	SMART
HX	213	256	3.76e-10	SMART
Blast:HX	369	422	2e-27	BLAST

Predicted Effect

unknown
Transcript: ENSMUST00000164600
AA Change: K1155R

SMART Domains

Protein: ENSMUSP00000128943
Gene: ENSMUSG00000006014
AA Change: K1155R

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
SO	26	68	9.21e-18	SMART
SO	69	108	2.77e-12	SMART
low complexity region	110	122	N/A	INTRINSIC
low complexity region	127	184	N/A	INTRINSIC
low complexity region	191	212	N/A	INTRINSIC
low complexity region	229	239	N/A	INTRINSIC
internal_repeat_3	244	271	7.42e-5	PROSPERO
low complexity region	277	309	N/A	INTRINSIC
Pfam:Cornifin	404	497	2.4e-14	PFAM
Pfam:Cornifin	468	584	3.2e-15	PFAM
Pfam:Cornifin	550	648	3.3e-16	PFAM
Pfam:Cornifin	625	722	2.1e-15	PFAM
Pfam:Cornifin	647	743	7.8e-16	PFAM
Pfam:Cornifin	706	822	1.4e-12	PFAM
low complexity region	826	879	N/A	INTRINSIC
internal_repeat_2	889	915	1.24e-5	PROSPERO
HX	967	1009	1.67e-7	SMART
HX	1011	1054	3.76e-10	SMART
Blast:HX	1167	1220	6e-27	BLAST

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Aging homozygous null mice develop a hopping gait, irregular endochondral growth plates, altered cartilage surface, camptodactyly, progressive synovial hyperplasia and, ultimately, joint failure. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 137,770,894 (GRCm39)	T28A	probably benign	Het
Adam15	T	C	3: 89,253,270 (GRCm39)	I220V	probably benign	Het
Atf7ip2	T	A	16: 10,058,512 (GRCm39)	V317E	probably benign	Het
Bin3	T	G	14: 70,367,009 (GRCm39)		probably null	Het
Bnip3l	G	A	14: 67,246,214 (GRCm39)	P7L	possibly damaging	Het
Brd2	T	C	17: 34,334,205 (GRCm39)	T286A	possibly damaging	Het
Cers6	A	G	2: 68,833,114 (GRCm39)	Y144C	probably benign	Het
Cox4i2	C	A	2: 152,602,610 (GRCm39)	N101K	probably damaging	Het
Dguok	T	A	6: 83,463,999 (GRCm39)	L186F	probably benign	Het
Dock8	A	G	19: 25,148,926 (GRCm39)	N1468S	probably null	Het
Eral1	T	C	11: 77,965,410 (GRCm39)	H335R		Het
Gm3248	A	T	14: 5,944,993 (GRCm38)	I63K	probably benign	Het
Gm3415	A	C	5: 146,493,376 (GRCm39)	I74L	probably benign	Het
Kdm5b	A	T	1: 134,558,240 (GRCm39)	R1416*	probably null	Het
Lrit2	T	A	14: 36,790,115 (GRCm39)	C28*	probably null	Het
Mctp1	A	T	13: 76,532,840 (GRCm39)	T63S	probably benign	Het
Ncbp3	T	A	11: 72,944,323 (GRCm39)	N108K	possibly damaging	Het
Nlrp4b	A	G	7: 10,448,651 (GRCm39)	I285V	probably benign	Het
Nup85	C	T	11: 115,457,471 (GRCm39)	R58W	probably benign	Het
Pcnx4	T	C	12: 72,613,792 (GRCm39)	V579A	probably benign	Het
Pde10a	T	C	17: 9,020,272 (GRCm39)	S70P	unknown	Het
Pfpl	T	C	19: 12,407,107 (GRCm39)	F453L	probably damaging	Het
Ppp3cb	C	A	14: 20,578,314 (GRCm39)	L145F	probably damaging	Het
Prkcb	G	T	7: 122,233,070 (GRCm39)	E656*	probably null	Het
Prrc2b	C	A	2: 32,103,199 (GRCm39)	H892Q	probably benign	Het
Pxk	T	C	14: 8,140,748 (GRCm38)		probably null	Het
Ruvbl1	T	C	6: 88,444,558 (GRCm39)	V51A	probably benign	Het
Ryr3	C	A	2: 112,560,845 (GRCm39)	R2972L	probably benign	Het
Sec14l1	A	G	11: 117,046,058 (GRCm39)	I542V	possibly damaging	Het
Selplg	GTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCT	GTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCT	5: 113,957,756 (GRCm39)		probably benign	Het
Sgk1	AAGA	AAGAGA	10: 21,868,290 (GRCm39)		probably null	Het
Slc26a9	C	A	1: 131,681,688 (GRCm39)	A167E	probably benign	Het
Tarbp1	A	T	8: 127,183,262 (GRCm39)	L519Q	probably null	Het
Trak2	G	A	1: 58,985,463 (GRCm39)	R12*	probably null	Het
Ush2a	A	G	1: 188,360,768 (GRCm39)	I2163V	probably benign	Het
Vmn2r114	T	A	17: 23,531,098 (GRCm39)	N64Y		Het
Wdfy4	T	C	14: 32,769,219 (GRCm39)	Y2236C		Het
Zfp316	A	T	5: 143,240,348 (GRCm39)	V557E	possibly damaging	Het

Other mutations in Prg4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00493:Prg4	APN	1	150,327,671 (GRCm39)	missense	probably damaging	0.99
IGL02033:Prg4	APN	1	150,331,619 (GRCm39)	intron	probably benign
IGL02154:Prg4	APN	1	150,330,613 (GRCm39)	intron	probably benign
IGL03111:Prg4	APN	1	150,327,653 (GRCm39)	missense	probably benign	0.06
IGL03177:Prg4	APN	1	150,331,354 (GRCm39)	intron	probably benign
IGL03260:Prg4	APN	1	150,331,378 (GRCm39)	intron	probably benign
IGL03281:Prg4	APN	1	150,325,839 (GRCm39)	splice site	probably benign
R0046:Prg4	UTSW	1	150,331,837 (GRCm39)	missense	possibly damaging	0.53
R0046:Prg4	UTSW	1	150,331,837 (GRCm39)	missense	possibly damaging	0.53
R0196:Prg4	UTSW	1	150,330,243 (GRCm39)	intron	probably benign
R0233:Prg4	UTSW	1	150,329,298 (GRCm39)	splice site	probably benign
R0255:Prg4	UTSW	1	150,331,558 (GRCm39)	intron	probably benign
R0616:Prg4	UTSW	1	150,336,462 (GRCm39)	missense	probably damaging	1.00
R1016:Prg4	UTSW	1	150,330,442 (GRCm39)	intron	probably benign
R1826:Prg4	UTSW	1	150,327,760 (GRCm39)	missense	probably benign	0.09
R1862:Prg4	UTSW	1	150,336,420 (GRCm39)	missense	probably damaging	0.99
R1863:Prg4	UTSW	1	150,336,420 (GRCm39)	missense	probably damaging	0.99
R1922:Prg4	UTSW	1	150,325,750 (GRCm39)	nonsense	probably null
R1940:Prg4	UTSW	1	150,331,774 (GRCm39)	missense	possibly damaging	0.53
R3765:Prg4	UTSW	1	150,327,122 (GRCm39)	missense	probably damaging	0.97
R3855:Prg4	UTSW	1	150,327,751 (GRCm39)	missense	probably damaging	1.00
R3894:Prg4	UTSW	1	150,330,510 (GRCm39)	intron	probably benign
R3895:Prg4	UTSW	1	150,330,510 (GRCm39)	intron	probably benign
R3912:Prg4	UTSW	1	150,327,619 (GRCm39)	missense	probably damaging	1.00
R3935:Prg4	UTSW	1	150,333,908 (GRCm39)	missense	possibly damaging	0.68
R4050:Prg4	UTSW	1	150,330,510 (GRCm39)	intron	probably benign
R4475:Prg4	UTSW	1	150,330,610 (GRCm39)	intron	probably benign
R4794:Prg4	UTSW	1	150,330,297 (GRCm39)	intron	probably benign
R4910:Prg4	UTSW	1	150,331,574 (GRCm39)	intron	probably benign
R4911:Prg4	UTSW	1	150,331,574 (GRCm39)	intron	probably benign
R4993:Prg4	UTSW	1	150,336,432 (GRCm39)	missense	probably damaging	1.00
R5378:Prg4	UTSW	1	150,330,977 (GRCm39)	intron	probably benign
R5381:Prg4	UTSW	1	150,330,204 (GRCm39)	intron	probably benign
R5452:Prg4	UTSW	1	150,331,519 (GRCm39)	intron	probably benign
R5870:Prg4	UTSW	1	150,331,300 (GRCm39)	nonsense	probably null
R5888:Prg4	UTSW	1	150,328,101 (GRCm39)	missense	probably damaging	1.00
R5929:Prg4	UTSW	1	150,329,880 (GRCm39)	missense	probably benign	0.01
R6058:Prg4	UTSW	1	150,327,197 (GRCm39)	missense	probably damaging	0.99
R6059:Prg4	UTSW	1	150,325,748 (GRCm39)	missense	possibly damaging	0.67
R6232:Prg4	UTSW	1	150,331,567 (GRCm39)	intron	probably benign
R6272:Prg4	UTSW	1	150,330,517 (GRCm39)	intron	probably benign
R6459:Prg4	UTSW	1	150,330,052 (GRCm39)	intron	probably benign
R6659:Prg4	UTSW	1	150,336,432 (GRCm39)	missense	probably damaging	1.00
R6663:Prg4	UTSW	1	150,330,852 (GRCm39)	intron	probably benign
R6882:Prg4	UTSW	1	150,329,246 (GRCm39)	missense	probably damaging	1.00
R6970:Prg4	UTSW	1	150,331,657 (GRCm39)	intron	probably benign
R7078:Prg4	UTSW	1	150,334,014 (GRCm39)	missense	possibly damaging	0.91
R7102:Prg4	UTSW	1	150,328,005 (GRCm39)	missense	probably damaging	1.00
R7264:Prg4	UTSW	1	150,329,818 (GRCm39)	missense	not run
R7487:Prg4	UTSW	1	150,331,656 (GRCm39)	missense	unknown
R7531:Prg4	UTSW	1	150,330,786 (GRCm39)	missense	unknown
R7651:Prg4	UTSW	1	150,330,696 (GRCm39)	missense	unknown
R7701:Prg4	UTSW	1	150,333,293 (GRCm39)	missense	possibly damaging	0.53
R8072:Prg4	UTSW	1	150,331,774 (GRCm39)	missense	possibly damaging	0.53
R8168:Prg4	UTSW	1	150,331,601 (GRCm39)	missense	unknown
R8248:Prg4	UTSW	1	150,330,877 (GRCm39)	missense	unknown
R8436:Prg4	UTSW	1	150,331,318 (GRCm39)	missense	unknown
R8460:Prg4	UTSW	1	150,331,692 (GRCm39)	missense	possibly damaging	0.83
R8514:Prg4	UTSW	1	150,330,396 (GRCm39)	missense	unknown
R8904:Prg4	UTSW	1	150,331,810 (GRCm39)	missense	possibly damaging	0.83
R9072:Prg4	UTSW	1	150,331,288 (GRCm39)	missense	unknown
R9073:Prg4	UTSW	1	150,331,288 (GRCm39)	missense	unknown
R9274:Prg4	UTSW	1	150,331,924 (GRCm39)	missense	possibly damaging	0.53
R9337:Prg4	UTSW	1	150,327,116 (GRCm39)	missense	probably damaging	1.00
R9488:Prg4	UTSW	1	150,327,024 (GRCm39)	missense	probably benign
R9613:Prg4	UTSW	1	150,331,660 (GRCm39)	missense	unknown
X0024:Prg4	UTSW	1	150,330,243 (GRCm39)	intron	probably benign

Predicted Primers

PCR Primer
(F):5'- AATTACACTTGCGCTTCCTCGG -3'
(R):5'- GCCATGAAAGTACTAACCATTTAGG -3'

Sequencing Primer
(F):5'- TCCTCGGGTGAGATCAACTTGAAG -3'
(R):5'- TGCCTTACTGAGTAATAACTAAGACC -3'

Posted On

2022-10-06