Mutagenetix > Incidental Mutation

Incidental Mutation 'R9337:Prg4'

707209

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

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.152) question?

Stock #

R9337 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

150449412-150466165 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 150451365 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 311 (Y311C)

Ref Sequence

ENSEMBL: ENSMUSP00000006171 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000006171
AA Change: Y311C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000006171
Gene: ENSMUSG00000006014
AA Change: Y311C

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: Y853C

SMART Domains

Protein: ENSMUSP00000107532
Gene: ENSMUSG00000006014
AA Change: Y853C

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: Y900C

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

SMART Domains

Protein: ENSMUSP00000107533
Gene: ENSMUSG00000006014
AA Change: Y900C

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

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: Y1109C

SMART Domains

Protein: ENSMUSP00000125677
Gene: ENSMUSG00000006014
AA Change: Y1109C

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 damaging
Transcript: ENSMUST00000162367
AA Change: Y311C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000125551
Gene: ENSMUSG00000006014
AA Change: Y311C

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: Y1109C

SMART Domains

Protein: ENSMUSP00000128943
Gene: ENSMUSG00000006014
AA Change: Y1109C

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

Meta Mutation Damage Score

0.4754

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

100% (65/65)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb9	T	C	5: 124,090,113	T22A	possibly damaging	Het
Adad1	T	C	3: 37,085,098	V439A	possibly damaging	Het
Ahnak	G	A	19: 9,012,460		probably benign	Het
Arhgef10l	G	A	4: 140,611,313	T46I	probably damaging	Het
BC022687	T	C	12: 112,812,278	L218P	probably damaging	Het
C3ar1	A	G	6: 122,850,319	V313A	probably benign	Het
Capn13	T	A	17: 73,326,472		probably null	Het
Ccdc30	T	A	4: 119,333,723		probably null	Het
Ccdc7a	T	C	8: 128,889,838	Q928R	probably benign	Het
Cept1	A	G	3: 106,505,259	L299S	possibly damaging	Het
Cnot1	T	C	8: 95,741,820	I1460M	probably damaging	Het
Col4a2	T	C	8: 11,429,346	L743P	probably benign	Het
Cop1	T	C	1: 159,244,651	V179A	probably benign	Het
Cpvl	A	G	6: 53,932,494	I219T	probably damaging	Het
Cyc1	T	C	15: 76,344,306	V45A	probably benign	Het
Dnhd1	T	A	7: 105,720,599	N4410K	probably benign	Het
Dok4	T	A	8: 94,866,841	T106S	probably benign	Het
Exosc10	T	C	4: 148,581,131	F842L	probably damaging	Het
Fam24b	T	A	7: 131,326,220	Y80F	probably benign	Het
Fbn2	G	A	18: 58,209,651	A52V	probably benign	Het
Gal3st3	A	T	19: 5,306,840	N81I	probably damaging	Het
Gm13283	T	A	4: 88,760,799	V9E	possibly damaging	Het
Gm17026	A	G	14: 42,258,916	S58P		Het
Grm8	A	T	6: 27,761,215	S337T	probably benign	Het
Hdac5	G	A	11: 102,205,352	P332S	probably damaging	Het
Hr	A	T	14: 70,559,884	E519V	probably benign	Het
Hspbap1	A	G	16: 35,825,025	H360R	probably benign	Het
Iqgap3	T	G	3: 88,116,118		probably null	Het
Krtap5-3	T	A	7: 142,202,530	H175Q	unknown	Het
Lrrn4	A	T	2: 132,870,632	S424T	probably benign	Het
Lsm10	C	A	4: 126,097,867	H5Q	probably damaging	Het
Megf10	A	T	18: 57,261,180	K459*	probably null	Het
Myo15b	A	C	11: 115,859,035	K210N		Het
Olfr1085	T	C	2: 86,658,132	T109A	probably benign	Het
Olfr1126	T	A	2: 87,457,183	I6N	probably benign	Het
Park7	A	T	4: 150,907,096	C46S	probably damaging	Het
Pik3cb	A	G	9: 99,061,791	F653S	probably damaging	Het
Plekha1	T	A	7: 130,909,618	C311S	possibly damaging	Het
Pprc1	T	A	19: 46,063,759	M576K	unknown	Het
Prelid3b	G	A	2: 174,468,368	T74M	probably benign	Het
Prom2	A	C	2: 127,529,174	V801G	probably damaging	Het
Psmd9	T	A	5: 123,248,324	V44D	probably damaging	Het
Ptpn3	C	G	4: 57,218,521	L647F	probably damaging	Het
Ptprj	T	C	2: 90,439,894	D1286G	probably damaging	Het
Rcc2	T	C	4: 140,718,378	I449T	probably damaging	Het
Rev3l	A	T	10: 39,822,854	S1116C	probably benign	Het
Rnf212	A	T	5: 108,774,889	S32T	possibly damaging	Het
Rnf40	T	A	7: 127,589,000	S2T	probably benign	Het
Rrp8	T	C	7: 105,734,177	D294G	probably damaging	Het
Rtf2	A	T	2: 172,466,285	K201N	probably damaging	Het
Runx3	A	G	4: 135,163,263	T173A	probably damaging	Het
Sardh	T	C	2: 27,196,666	I827M	probably benign	Het
Sec22b	T	C	3: 97,921,178	Y186H	probably benign	Het
Serpina5	C	T	12: 104,105,283	T383I	possibly damaging	Het
Slc12a2	A	G	18: 57,930,166	D906G	probably damaging	Het
Socs1	T	C	16: 10,784,714	D53G	possibly damaging	Het
Stat1	G	T	1: 52,152,270	A595S	probably benign	Het
Stat3	A	T	11: 100,907,989		probably null	Het
Styxl1	T	C	5: 135,765,738	S82G	probably benign	Het
Taf1b	T	A	12: 24,547,122	D353E	possibly damaging	Het
Tbce	T	C	13: 14,019,813	K87R	probably benign	Het
Thada	T	C	17: 84,441,777	M589V	probably benign	Het
Them5	A	G	3: 94,346,741	M257V	unknown	Het
Tln1	A	T	4: 43,532,927	I2425N	probably damaging	Het
Tuba8	A	G	6: 121,225,864	S379G	probably damaging	Het
Vrk1	T	C	12: 106,058,698		probably null	Het
Zbtb34	T	C	2: 33,411,704	Y275C	probably damaging	Het
Zcwpw1	T	C	5: 137,801,012	C214R	probably benign	Het
Zeb2	A	G	2: 45,022,900	V137A	probably benign	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
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
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'- CTAAATGGTTAGTACTTTCATGGCC -3'
(R):5'- GAACGGCATTAAAAGTAGCCATTAC -3'

Sequencing Primer
(F):5'- GGTTAGTACTTTCATGGCCAATAC -3'
(R):5'- GTGGCAACATTCAGCAGT -3'

Posted On

2022-04-18