Mutagenetix > Incidental Mutation

Incidental Mutation 'R6059:Prg4'

483101

Institutional Source

Beutler Lab

Gene Symbol

Prg4

Ensembl Gene

ENSMUSG00000006014

Gene Name

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

Synonyms

DOL54, SZP, lubricin, MSF

MMRRC Submission

044225-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.174) question?

Stock #

R6059 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

150449412-150466165 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 150449997 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 1009 (Y1009F)

Ref Sequence

ENSEMBL: ENSMUSP00000107533 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000006171
AA Change: Y420F

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

SMART Domains

Protein: ENSMUSP00000006171
Gene: ENSMUSG00000006014
AA Change: Y420F

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: Y962F

SMART Domains

Protein: ENSMUSP00000107532
Gene: ENSMUSG00000006014
AA Change: Y962F

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

possibly damaging
Transcript: ENSMUST00000111902
AA Change: Y1009F

PolyPhen 2 Score 0.670 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000107533
Gene: ENSMUSG00000006014
AA Change: Y1009F

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

noncoding transcript
Transcript: ENSMUST00000128417

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130779

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138718

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152967

Predicted Effect

unknown
Transcript: ENSMUST00000164600
AA Change: Y1218F

SMART Domains

Protein: ENSMUSP00000128943
Gene: ENSMUSG00000006014
AA Change: Y1218F

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

Predicted Effect

unknown
Transcript: ENSMUST00000161611
AA Change: Y1218F

SMART Domains

Protein: ENSMUSP00000125677
Gene: ENSMUSG00000006014
AA Change: Y1218F

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

possibly damaging
Transcript: ENSMUST00000162367
AA Change: Y420F

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

SMART Domains

Protein: ENSMUSP00000125551
Gene: ENSMUSG00000006014
AA Change: Y420F

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

Meta Mutation Damage Score

0.0950

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.8%
20x: 93.3%

Validation Efficiency

95% (54/57)

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700067P10Rik	C	A	17: 48,090,327	T44K	probably benign	Het
4931406P16Rik	G	A	7: 34,245,463	A452V	possibly damaging	Het
Ablim2	A	G	5: 35,857,164	D189G	probably benign	Het
Abo	A	G	2: 26,843,353	V278A	possibly damaging	Het
Anxa1	A	G	19: 20,377,700	F237L	possibly damaging	Het
Atp11b	A	G	3: 35,814,177	Y466C	possibly damaging	Het
Cfh	T	A	1: 140,118,690	K531N	possibly damaging	Het
Cgref1	G	T	5: 30,945,384	P31Q	probably damaging	Het
Clca3a2	G	A	3: 144,810,770	A355V	probably damaging	Het
Cntnap5c	T	A	17: 58,313,712	C929S	probably damaging	Het
Col6a6	A	T	9: 105,783,917	V331D	probably damaging	Het
Cyp4a12b	T	A	4: 115,438,104	V469E	possibly damaging	Het
Dchs2	A	G	3: 83,355,736	S3104G	probably benign	Het
Ddx24	G	T	12: 103,408,300	A875E	probably damaging	Het
Dsc1	A	T	18: 20,110,242	N51K	probably damaging	Het
Epb41l3	A	G	17: 69,284,642	E708G	probably damaging	Het
Epb41l3	C	T	17: 69,286,798	T537I	probably damaging	Het
Fam162b	A	T	10: 51,590,307	C39S	probably benign	Het
Gbf1	T	C	19: 46,265,248	I531T	probably damaging	Het
Glipr1l2	T	C	10: 112,083,518	V48A	probably benign	Het
Gm11639	T	C	11: 105,036,769	I4788T	probably benign	Het
Gm13023	T	G	4: 143,793,980	S101A	possibly damaging	Het
Gorasp1	A	G	9: 119,930,006	V177A	probably damaging	Het
Gys1	A	G	7: 45,455,288		probably null	Het
Hif1a	T	A	12: 73,941,800	V523E	probably damaging	Het
Hnrnph3	A	T	10: 63,018,862		probably benign	Het
Lcn9	C	A	2: 25,824,725	L159I	possibly damaging	Het
Luzp1	C	T	4: 136,541,480	A338V	probably benign	Het
Map3k10	A	T	7: 27,656,822	S891T	probably damaging	Het
Mmrn2	C	T	14: 34,397,591	Q97*	probably null	Het
Mov10	G	A	3: 104,817,950		probably benign	Het
Ncam1	A	C	9: 49,544,666	Y551D	probably damaging	Het
Ncf1	A	T	5: 134,223,487	Y237N	probably damaging	Het
Nipbl	A	T	15: 8,295,568	I2537N	probably damaging	Het
Nlrp1b	A	T	11: 71,217,010	V555E	possibly damaging	Het
Nod2	T	C	8: 88,664,414	Y428H	probably damaging	Het
Nup133	C	A	8: 123,914,596	A862S	probably damaging	Het
Pcdhgb2	T	A	18: 37,690,025	L23*	probably null	Het
Pclo	A	G	5: 14,811,700	E4889G	unknown	Het
Plcd3	T	A	11: 103,080,401	I110F	possibly damaging	Het
Plxna2	C	A	1: 194,810,971	N1851K	possibly damaging	Het
Ppp2r5c	C	A	12: 110,574,788	A457E	probably benign	Het
Ppp5c	C	T	7: 17,027,907		probably benign	Het
Rcor3	A	T	1: 192,119,940	M303K	probably benign	Het
Rrn3	G	A	16: 13,806,604	M433I	probably benign	Het
Serpinb9e	G	A	13: 33,257,774	V230M	probably benign	Het
Shisa6	T	A	11: 66,224,974	H279L	probably damaging	Het
Slc38a11	A	T	2: 65,334,745	I234N	probably damaging	Het
Socs1	G	C	16: 10,784,530	F114L	probably damaging	Het
Ssc5d	C	T	7: 4,942,744	T925M	possibly damaging	Het
Stc1	T	C	14: 69,032,438	S156P	probably damaging	Het
Ttc5	C	G	14: 50,777,846	V103L	probably damaging	Het
Vmn1r73	A	G	7: 11,756,611	T119A	probably benign	Het
Vmn2r99	G	A	17: 19,378,980	D309N	probably benign	Het
Vps53	T	C	11: 76,066,867	H353R	possibly damaging	Het
Ythdf3	T	A	3: 16,203,192	Y47*	probably null	Het
Zfp276	T	C	8: 123,267,823	M543T	probably damaging	Het

Other mutations in Prg4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00493:Prg4	APN	1	150451920	missense	probably damaging	0.99
IGL02033:Prg4	APN	1	150455868	intron	probably benign
IGL02154:Prg4	APN	1	150454862	intron	probably benign
IGL03111:Prg4	APN	1	150451902	missense	probably benign	0.06
IGL03177:Prg4	APN	1	150455603	intron	probably benign
IGL03260:Prg4	APN	1	150455627	intron	probably benign
IGL03281:Prg4	APN	1	150450088	splice site	probably benign
R0046:Prg4	UTSW	1	150456086	missense	possibly damaging	0.53
R0046:Prg4	UTSW	1	150456086	missense	possibly damaging	0.53
R0196:Prg4	UTSW	1	150454492	intron	probably benign
R0233:Prg4	UTSW	1	150453547	splice site	probably benign
R0255:Prg4	UTSW	1	150455807	intron	probably benign
R0616:Prg4	UTSW	1	150460711	missense	probably damaging	1.00
R1016:Prg4	UTSW	1	150454691	intron	probably benign
R1826:Prg4	UTSW	1	150452009	missense	probably benign	0.09
R1862:Prg4	UTSW	1	150460669	missense	probably damaging	0.99
R1863:Prg4	UTSW	1	150460669	missense	probably damaging	0.99
R1922:Prg4	UTSW	1	150449999	nonsense	probably null
R1940:Prg4	UTSW	1	150456023	missense	possibly damaging	0.53
R3765:Prg4	UTSW	1	150451371	missense	probably damaging	0.97
R3855:Prg4	UTSW	1	150452000	missense	probably damaging	1.00
R3894:Prg4	UTSW	1	150454759	intron	probably benign
R3895:Prg4	UTSW	1	150454759	intron	probably benign
R3912:Prg4	UTSW	1	150451868	missense	probably damaging	1.00
R3935:Prg4	UTSW	1	150458157	missense	possibly damaging	0.68
R4050:Prg4	UTSW	1	150454759	intron	probably benign
R4475:Prg4	UTSW	1	150454859	intron	probably benign
R4794:Prg4	UTSW	1	150454546	intron	probably benign
R4910:Prg4	UTSW	1	150455823	intron	probably benign
R4911:Prg4	UTSW	1	150455823	intron	probably benign
R4993:Prg4	UTSW	1	150460681	missense	probably damaging	1.00
R5378:Prg4	UTSW	1	150455226	intron	probably benign
R5381:Prg4	UTSW	1	150454453	intron	probably benign
R5452:Prg4	UTSW	1	150455768	intron	probably benign
R5870:Prg4	UTSW	1	150455549	nonsense	probably null
R5888:Prg4	UTSW	1	150452350	missense	probably damaging	1.00
R5929:Prg4	UTSW	1	150454129	missense	probably benign	0.01
R6058:Prg4	UTSW	1	150451446	missense	probably damaging	0.99
R6232:Prg4	UTSW	1	150455816	intron	probably benign
R6272:Prg4	UTSW	1	150454766	intron	probably benign
R6459:Prg4	UTSW	1	150454301	intron	probably benign
R6659:Prg4	UTSW	1	150460681	missense	probably damaging	1.00
R6663:Prg4	UTSW	1	150455101	intron	probably benign
R6882:Prg4	UTSW	1	150453495	missense	probably damaging	1.00
R6970:Prg4	UTSW	1	150455906	intron	probably benign
R7078:Prg4	UTSW	1	150458263	missense	possibly damaging	0.91
R7102:Prg4	UTSW	1	150452254	missense	probably damaging	1.00
R7264:Prg4	UTSW	1	150454067	missense	not run
R7487:Prg4	UTSW	1	150455905	missense	unknown
R7531:Prg4	UTSW	1	150455035	missense	unknown
R7651:Prg4	UTSW	1	150454945	missense	unknown
R7701:Prg4	UTSW	1	150457542	missense	possibly damaging	0.53
R8072:Prg4	UTSW	1	150456023	missense	possibly damaging	0.53
R8168:Prg4	UTSW	1	150455850	missense	unknown
R8248:Prg4	UTSW	1	150455126	missense	unknown
R8436:Prg4	UTSW	1	150455567	missense	unknown
R8460:Prg4	UTSW	1	150455941	missense	possibly damaging	0.83
R8514:Prg4	UTSW	1	150454645	missense	unknown
R8904:Prg4	UTSW	1	150456059	missense	possibly damaging	0.83
R9072:Prg4	UTSW	1	150455537	missense	unknown
R9073:Prg4	UTSW	1	150455537	missense	unknown
R9274:Prg4	UTSW	1	150456173	missense	possibly damaging	0.53
R9337:Prg4	UTSW	1	150451365	missense	probably damaging	1.00
R9488:Prg4	UTSW	1	150451273	missense	probably benign
R9613:Prg4	UTSW	1	150455909	missense	unknown
R9670:Prg4	UTSW	1	150450867	missense	probably benign	0.01
X0024:Prg4	UTSW	1	150454492	intron	probably benign

Predicted Primers

PCR Primer
(F):5'- GTGACACATGTGAATAAGATTGACG -3'
(R):5'- GGATGCTGAAAAGTTATTCCTTCCATC -3'

Sequencing Primer
(F):5'- ACATGTGAATAAGATTGACGAATCTG -3'
(R):5'- TGTCAGAAAGTTAATGACATCCAC -3'

Posted On

2017-07-14