Mutagenetix > Incidental Mutation

Incidental Mutation 'R3912:Prg4'

309433

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

040910-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.155) question?

Stock #

R3912 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

150449412-150466165 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 150451868 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 278 (Y278C)

Ref Sequence

ENSEMBL: ENSMUSP00000125551 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006171] [ENSMUST00000111901] [ENSMUST00000111902] [ENSMUST00000119161] [ENSMUST00000124484] [ENSMUST00000124973] [ENSMUST00000161320] [ENSMUST00000161611] [ENSMUST00000164600] [ENSMUST00000162367]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000006171
AA Change: Y278C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000006171
Gene: ENSMUSG00000006014
AA Change: Y278C

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: Y820C

SMART Domains

Protein: ENSMUSP00000107532
Gene: ENSMUSG00000006014
AA Change: Y820C

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 damaging
Transcript: ENSMUST00000111902
AA Change: Y867C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000107533
Gene: ENSMUSG00000006014
AA Change: Y867C

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

probably benign
Transcript: ENSMUST00000161320

SMART Domains

Protein: ENSMUSP00000124801
Gene: ENSMUSG00000006014

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
SO	25	67	3.83e-15	SMART
low complexity region	69	83	N/A	INTRINSIC
low complexity region	100	110	N/A	INTRINSIC
low complexity region	148	179	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000161611
AA Change: Y1076C

SMART Domains

Protein: ENSMUSP00000125677
Gene: ENSMUSG00000006014
AA Change: Y1076C

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

unknown
Transcript: ENSMUST00000164600
AA Change: Y1076C

SMART Domains

Protein: ENSMUSP00000128943
Gene: ENSMUSG00000006014
AA Change: Y1076C

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

probably damaging
Transcript: ENSMUST00000162367
AA Change: Y278C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000125551
Gene: ENSMUSG00000006014
AA Change: Y278C

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

0.7893

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.8%

Validation Efficiency

100% (56/56)

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010111I01Rik	G	T	13: 63,156,706	E402*	probably null	Het
9030624J02Rik	A	G	7: 118,746,390	T49A	possibly damaging	Het
Acot1	A	G	12: 84,017,032	S305G	probably damaging	Het
Acot12	A	G	13: 91,770,089	D167G	probably benign	Het
Adgra1	T	C	7: 139,845,714		probably null	Het
Adh7	T	A	3: 138,221,780	V29E	probably damaging	Het
Atp2c2	A	G	8: 119,721,276	K103E	probably damaging	Het
Camkk1	A	G	11: 73,033,816	D285G	probably benign	Het
Ccdc158	G	C	5: 92,648,935	T514S	possibly damaging	Het
Cdhr5	T	A	7: 141,273,857	D210V	probably damaging	Het
Cndp1	C	T	18: 84,631,999	D190N	probably benign	Het
Eepd1	C	T	9: 25,483,304	T288M	probably damaging	Het
Erbin	G	A	13: 103,886,338		probably benign	Het
Erbin	G	T	13: 103,862,287	T197K	probably benign	Het
Fnip2	A	T	3: 79,479,505	D971E	possibly damaging	Het
Gab2	A	G	7: 97,299,073	Y290C	probably damaging	Het
Gbp3	C	T	3: 142,566,338		probably benign	Het
Gm14326	T	C	2: 177,945,865	K446R	probably damaging	Het
Gm5724	A	G	6: 141,727,636	F392S	probably damaging	Het
Herc2	T	C	7: 56,098,437	Y518H	probably damaging	Het
Id2	T	A	12: 25,095,872	K47*	probably null	Het
Ilf2	A	G	3: 90,487,060	N295S	probably benign	Het
Ilf3	C	T	9: 21,398,126	A526V	possibly damaging	Het
Ints10	T	A	8: 68,813,620	S478T	probably damaging	Het
Kirrel	C	T	3: 87,089,151	M380I	probably null	Het
Lrrc7	G	A	3: 158,291,952	L158F	probably damaging	Het
Mroh9	C	T	1: 163,066,069	C179Y	probably damaging	Het
Mrps18b	C	T	17: 35,910,939	V165I	probably benign	Het
Myrip	A	G	9: 120,432,616	S432G	probably benign	Het
Nutm2	C	T	13: 50,472,940	A377V	possibly damaging	Het
Olfr700	A	T	7: 106,805,865	V199D	probably damaging	Het
Pate4	C	A	9: 35,611,844	M1I	probably null	Het
Pax7	C	A	4: 139,780,898	W272L	probably benign	Het
Ppp1r12b	C	T	1: 134,887,318	E320K	probably damaging	Het
Pvr	T	C	7: 19,909,292	N339D	probably benign	Het
Rev3l	A	G	10: 39,820,556	I521M	probably damaging	Het
Ryr2	A	G	13: 11,772,427	I1020T	probably damaging	Het
Scn4a	T	A	11: 106,320,716	I1492F	probably damaging	Het
Sec16a	C	T	2: 26,414,387	G2304D	probably damaging	Het
Shisa7	T	A	7: 4,830,240	R341*	probably null	Het
Slc19a3	T	A	1: 83,022,703	M198L	probably benign	Het
Slc26a8	T	A	17: 28,644,779	N669Y	possibly damaging	Het
Snap91	T	C	9: 86,792,557	T534A	possibly damaging	Het
Susd4	A	T	1: 182,887,466	Y284F	probably damaging	Het
Tas1r1	A	T	4: 152,031,924	Y418N	probably damaging	Het
Tdrd12	A	G	7: 35,487,713	I584T	probably damaging	Het
Tmtc3	A	C	10: 100,449,026	N582K	probably damaging	Het
Tnfrsf11b	G	A	15: 54,256,182		probably benign	Het
Trim30a	A	G	7: 104,411,141	V476A	probably damaging	Het
Vmn1r39	C	T	6: 66,805,141	M27I	probably benign	Het
Vmn2r59	T	C	7: 42,046,320	T223A	probably benign	Het
Vwa5a	T	C	9: 38,734,743	I469T	probably damaging	Het
Wnt3a	A	C	11: 59,250,002	D229E	possibly 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
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
R6059:Prg4	UTSW	1	150449997	missense	possibly damaging	0.67
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'- AAAGTCCAGTTGTTTGATGGTTCAC -3'
(R):5'- GGATGAATTCCTGAAACATGCCTAC -3'

Sequencing Primer
(F):5'- TGATGGTTCACATTTCAGGAAATC -3'
(R):5'- TGCCTACAAAACCTTTGACATC -3'

Posted On

2015-04-17