Mutagenetix > Incidental Mutation

Incidental Mutation 'R1997:Prdm5'

224330

Institutional Source

Beutler Lab

Gene Symbol

Prdm5

Ensembl Gene

ENSMUSG00000029913

Gene Name

PR domain containing 5

Synonyms

6530401I24Rik, PFM2, E130112L17Rik, 4432417F03Rik

MMRRC Submission

040007-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1997 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

65755972-65913994 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 65913072 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 207 (Y207C)

Ref Sequence

ENSEMBL: ENSMUSP00000079979 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031973] [ENSMUST00000031976] [ENSMUST00000081219] [ENSMUST00000172638]

AlphaFold

Q9CXE0

Predicted Effect

probably damaging
Transcript: ENSMUST00000031973
AA Change: Y401C

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

SMART Domains

Protein: ENSMUSP00000031973
Gene: ENSMUSG00000029913
AA Change: Y401C

Domain	Start	End	E-Value	Type
PDB:3EP0\|B	4	101	1e-11	PDB
Blast:SET	8	100	4e-64	BLAST
ZnF_C2H2	105	127	3.16e-3	SMART
ZnF_C2H2	133	155	8.81e-2	SMART
ZnF_C2H2	161	183	1.95e-3	SMART
ZnF_C2H2	189	211	6.78e-3	SMART
ZnF_C2H2	217	240	1.2e-3	SMART
ZnF_C2H2	246	268	4.87e-4	SMART
ZnF_C2H2	274	296	2.4e-3	SMART
ZnF_C2H2	302	324	2.43e-4	SMART
ZnF_C2H2	330	352	3.21e-4	SMART
ZnF_C2H2	358	380	1.45e-2	SMART
ZnF_C2H2	387	410	1.43e-1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000031976
AA Change: Y585C

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

SMART Domains

Protein: ENSMUSP00000031976
Gene: ENSMUSG00000029913
AA Change: Y585C

Domain	Start	End	E-Value	Type
SET	8	130	2.01e-4	SMART
ZnF_C2H2	167	190	3.39e-3	SMART
ZnF_C2H2	199	221	1.04e-3	SMART
ZnF_C2H2	231	256	1.26e-2	SMART
ZnF_C2H2	264	286	1.95e-3	SMART
ZnF_C2H2	289	311	3.16e-3	SMART
ZnF_C2H2	317	339	8.81e-2	SMART
ZnF_C2H2	345	367	1.95e-3	SMART
ZnF_C2H2	373	395	6.78e-3	SMART
ZnF_C2H2	401	424	1.2e-3	SMART
ZnF_C2H2	430	452	4.87e-4	SMART
ZnF_C2H2	458	480	2.4e-3	SMART
ZnF_C2H2	486	508	2.43e-4	SMART
ZnF_C2H2	514	536	3.21e-4	SMART
ZnF_C2H2	542	564	1.45e-2	SMART
ZnF_C2H2	571	594	1.43e-1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000081219
AA Change: Y207C

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

SMART Domains

Protein: ENSMUSP00000079979
Gene: ENSMUSG00000029913
AA Change: Y207C

Domain	Start	End	E-Value	Type
Blast:SET	8	72	2e-34	BLAST
ZnF_C2H2	80	102	2.4e-3	SMART
ZnF_C2H2	108	130	2.43e-4	SMART
ZnF_C2H2	136	158	3.21e-4	SMART
ZnF_C2H2	164	186	1.45e-2	SMART
ZnF_C2H2	193	216	1.43e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000172638

SMART Domains

Protein: ENSMUSP00000133423
Gene: ENSMUSG00000029913

Domain	Start	End	E-Value	Type
SET	8	130	2.01e-4	SMART
ZnF_C2H2	167	190	3.39e-3	SMART
ZnF_C2H2	199	221	1.04e-3	SMART
ZnF_C2H2	231	256	1.26e-2	SMART
ZnF_C2H2	264	286	1.95e-3	SMART
ZnF_C2H2	289	311	3.16e-3	SMART
ZnF_C2H2	317	339	8.81e-2	SMART
ZnF_C2H2	345	367	1.95e-3	SMART
ZnF_C2H2	373	395	6.78e-3	SMART
ZnF_C2H2	401	424	1.2e-3	SMART
ZnF_C2H2	430	452	4.87e-4	SMART
ZnF_C2H2	458	480	2.4e-3	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205155

Meta Mutation Damage Score

0.1522

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a hypomorphic allele display delayed bone ossification with reduced collagen fibril formation, total bone area, bone mineral content and bone mineral density. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	A	G	14: 32,382,005 (GRCm39)	F1320S	possibly damaging	Het
Aaas	C	T	15: 102,248,494 (GRCm39)	V241I	probably benign	Het
Abca17	A	G	17: 24,504,700 (GRCm39)	I1233T	probably benign	Het
Acin1	T	C	14: 54,884,156 (GRCm39)		probably null	Het
Acly	A	T	11: 100,409,977 (GRCm39)	I185N	probably damaging	Het
Adamts16	T	C	13: 70,901,386 (GRCm39)	D897G	probably benign	Het
Allc	A	C	12: 28,613,482 (GRCm39)	D153E	probably benign	Het
Ankrd12	A	G	17: 66,291,879 (GRCm39)	S1185P	probably damaging	Het
Aoc1l2	A	T	6: 48,909,363 (GRCm39)	Q536L	probably damaging	Het
Ap1g2	T	C	14: 55,339,835 (GRCm39)	E448G	probably benign	Het
Atg9a	A	T	1: 75,166,270 (GRCm39)	V50D	probably benign	Het
Bace2	A	T	16: 97,216,289 (GRCm39)	D294V	possibly damaging	Het
Camsap2	T	C	1: 136,199,283 (GRCm39)	K708E	probably damaging	Het
Card10	G	A	15: 78,678,175 (GRCm39)	R358C	probably damaging	Het
Ccdc81	A	T	7: 89,547,271 (GRCm39)	V39E	probably damaging	Het
Cdh20	A	T	1: 109,976,668 (GRCm39)	D111V	probably damaging	Het
Cercam	C	A	2: 29,762,935 (GRCm39)	T223K	probably benign	Het
Cimip2a	T	G	2: 25,110,217 (GRCm39)	L43R	probably damaging	Het
Cog5	A	G	12: 31,710,848 (GRCm39)	H76R	possibly damaging	Het
Col28a1	A	T	6: 7,999,644 (GRCm39)	N1024K	probably benign	Het
Csrnp3	A	T	2: 65,779,446 (GRCm39)	N41Y	probably damaging	Het
Cyp2t4	G	A	7: 26,857,038 (GRCm39)		probably null	Het
Dbn1	T	C	13: 55,630,254 (GRCm39)	H38R	probably damaging	Het
Dclre1b	A	G	3: 103,710,672 (GRCm39)	V287A	probably benign	Het
Dennd4c	A	G	4: 86,755,634 (GRCm39)	T1609A	probably benign	Het
Depdc5	T	A	5: 33,059,250 (GRCm39)		probably null	Het
Dhcr7	T	G	7: 143,401,167 (GRCm39)	D446E	probably damaging	Het
Dlx5	A	T	6: 6,879,680 (GRCm39)	M129K	possibly damaging	Het
Dnah11	C	G	12: 118,046,203 (GRCm39)	G1745A	possibly damaging	Het
Dnm3	T	C	1: 162,181,281 (GRCm39)	T133A	possibly damaging	Het
Eif3e	A	G	15: 43,129,005 (GRCm39)	L205P	probably damaging	Het
Fam91a1	A	G	15: 58,296,044 (GRCm39)		probably null	Het
Fank1	C	T	7: 133,463,954 (GRCm39)	T50I	probably damaging	Het
Fhod3	A	G	18: 25,223,473 (GRCm39)	T940A	possibly damaging	Het
Fkbp10	T	C	11: 100,306,841 (GRCm39)	F78L	probably damaging	Het
Gabbr2	A	C	4: 46,787,502 (GRCm39)	F387C	probably damaging	Het
Ggnbp2	A	T	11: 84,751,387 (GRCm39)	L138I	probably damaging	Het
Gm2832	T	A	14: 41,002,943 (GRCm39)		probably null	Het
Gm5084	T	A	13: 60,360,344 (GRCm39)		noncoding transcript	Het
Gm9979	T	C	13: 40,859,228 (GRCm39)		noncoding transcript	Het
Hepacam2	A	G	6: 3,487,241 (GRCm39)	S39P	probably damaging	Het
Hesx1	A	T	14: 26,723,340 (GRCm39)	N57Y	probably damaging	Het
Kcnh1	G	A	1: 191,959,243 (GRCm39)	V266I	probably damaging	Het
Kif24	T	C	4: 41,392,904 (GRCm39)	T1168A	possibly damaging	Het
Kng2	A	T	16: 22,843,626 (GRCm39)	F118I	possibly damaging	Het
Lig3	C	T	11: 82,678,492 (GRCm39)	P245S	probably benign	Het
Loxhd1	G	T	18: 77,383,465 (GRCm39)	W121C	probably damaging	Het
Ltn1	A	G	16: 87,178,525 (GRCm39)	V1568A	probably damaging	Het
Map3k4	A	T	17: 12,473,882 (GRCm39)		probably null	Het
Mcm10	C	T	2: 4,998,571 (GRCm39)	V790M	probably damaging	Het
Mia3	A	T	1: 183,125,707 (GRCm39)	F1223I	possibly damaging	Het
Mlec	C	A	5: 115,288,405 (GRCm39)	K150N	probably damaging	Het
Morn4	T	C	19: 42,064,977 (GRCm39)	K70R	possibly damaging	Het
Mphosph10	A	C	7: 64,037,195 (GRCm39)		probably null	Het
Myocd	G	A	11: 65,095,147 (GRCm39)	Q47*	probably null	Het
Nav2	T	A	7: 49,198,219 (GRCm39)	S1283T	probably benign	Het
Nbeal2	T	C	9: 110,461,266 (GRCm39)	H1599R	probably damaging	Het
Nek10	G	T	14: 14,827,003 (GRCm38)	G67V	probably benign	Het
Nlgn2	A	C	11: 69,718,876 (GRCm39)	V271G	probably damaging	Het
Or1o2	A	G	17: 37,542,523 (GRCm39)	V246A	probably damaging	Het
Or2l5	A	C	16: 19,333,792 (GRCm39)	V198G	probably damaging	Het
Pcolce2	A	T	9: 95,576,793 (GRCm39)	M355L	probably benign	Het
Per2	T	C	1: 91,368,581 (GRCm39)	E264G	probably damaging	Het
Phf2	A	G	13: 48,982,384 (GRCm39)	L113P	unknown	Het
Piwil2	A	G	14: 70,664,107 (GRCm39)	V14A	possibly damaging	Het
Plekha6	G	A	1: 133,191,556 (GRCm39)	A146T	probably benign	Het
Plxnb2	C	T	15: 89,042,971 (GRCm39)	V1473I	probably benign	Het
Pms2	T	C	5: 143,850,518 (GRCm39)	L111P	probably damaging	Het
Polg	A	G	7: 79,108,979 (GRCm39)	L533P	probably damaging	Het
Ppp1r12b	A	G	1: 134,774,093 (GRCm39)		probably benign	Het
Ppp2r1b	T	A	9: 50,778,671 (GRCm39)	M208K	possibly damaging	Het
Prkar2b	A	G	12: 32,013,934 (GRCm39)	V314A	probably damaging	Het
Proser1	T	A	3: 53,386,292 (GRCm39)	S725T	probably benign	Het
Psg20	A	G	7: 18,416,535 (GRCm39)	F194L	probably benign	Het
Ptprz1	A	G	6: 23,050,496 (GRCm39)	I2255V	probably damaging	Het
Sardh	T	G	2: 27,134,409 (GRCm39)	T36P	probably damaging	Het
Sec23a	T	A	12: 59,048,793 (GRCm39)	I110L	probably benign	Het
Slc22a29	T	A	19: 8,195,162 (GRCm39)	I158L	probably benign	Het
Slc35c1	T	C	2: 92,284,984 (GRCm39)	D210G	probably benign	Het
Syde2	A	G	3: 145,704,746 (GRCm39)	N566S	probably benign	Het
Tcf20	G	A	15: 82,741,431 (GRCm39)	Q7*	probably null	Het
Terb2	T	A	2: 122,035,338 (GRCm39)	H186Q	possibly damaging	Het
Tet2	G	A	3: 133,192,350 (GRCm39)	Q695*	probably null	Het
Tnfaip1	T	C	11: 78,420,973 (GRCm39)	Y29C	probably damaging	Het
Traf3	A	G	12: 111,227,095 (GRCm39)	K328E	probably benign	Het
Uaca	A	G	9: 60,777,623 (GRCm39)	E668G	probably damaging	Het
Ube2o	T	A	11: 116,436,163 (GRCm39)	E326V	probably damaging	Het
Ubr1	C	T	2: 120,776,754 (GRCm39)		probably null	Het
Vmn1r19	T	A	6: 57,382,033 (GRCm39)	S195R	probably damaging	Het
Vmn1r213	T	G	13: 23,196,473 (GRCm39)	V352G	probably benign	Het
Vmn2r19	T	A	6: 123,292,880 (GRCm39)	D307E	probably damaging	Het
Wdfy3	T	C	5: 102,116,812 (GRCm39)	D76G	probably damaging	Het
Zan	A	T	5: 137,401,376 (GRCm39)	C4114*	probably null	Het
Zbed6	A	G	1: 133,584,451 (GRCm39)	L962P	probably damaging	Het
Zdhhc23	A	T	16: 43,799,305 (GRCm39)	C37S	probably damaging	Het
Zfp628	G	T	7: 4,921,831 (GRCm39)	G18W	probably damaging	Het
Zfp712	T	A	13: 67,190,114 (GRCm39)	K138*	probably null	Het
Zfp867	A	T	11: 59,354,417 (GRCm39)	V304D	probably damaging	Het
Zfp870	T	C	17: 33,103,027 (GRCm39)	T102A	possibly damaging	Het
Zmym5	G	A	14: 57,035,210 (GRCm39)	S286L	possibly damaging	Het

Other mutations in Prdm5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01395:Prdm5	APN	6	65,847,374 (GRCm39)	missense	possibly damaging	0.93
IGL02363:Prdm5	APN	6	65,771,303 (GRCm39)	missense	probably damaging	1.00
IGL02457:Prdm5	APN	6	65,858,100 (GRCm39)	missense	probably damaging	1.00
IGL03190:Prdm5	APN	6	65,833,116 (GRCm39)	splice site	probably benign
IGL03239:Prdm5	APN	6	65,863,062 (GRCm39)	splice site	probably benign
IGL03377:Prdm5	APN	6	65,836,457 (GRCm39)	missense	possibly damaging	0.93
R0329:Prdm5	UTSW	6	65,839,887 (GRCm39)	splice site	probably benign
R0926:Prdm5	UTSW	6	65,860,531 (GRCm39)	missense	probably damaging	0.99
R1458:Prdm5	UTSW	6	65,860,585 (GRCm39)	missense	probably damaging	0.99
R1859:Prdm5	UTSW	6	65,808,263 (GRCm39)	missense	probably benign	0.03
R1956:Prdm5	UTSW	6	65,913,060 (GRCm39)	missense	probably damaging	1.00
R1996:Prdm5	UTSW	6	65,913,072 (GRCm39)	missense	probably damaging	1.00
R2019:Prdm5	UTSW	6	65,808,340 (GRCm39)	missense	probably damaging	0.99
R3082:Prdm5	UTSW	6	65,913,069 (GRCm39)	missense	probably damaging	1.00
R3819:Prdm5	UTSW	6	65,913,041 (GRCm39)	missense	possibly damaging	0.92
R4411:Prdm5	UTSW	6	65,878,771 (GRCm39)	nonsense	probably null
R4981:Prdm5	UTSW	6	65,847,446 (GRCm39)	missense	probably damaging	0.99
R5077:Prdm5	UTSW	6	65,756,158 (GRCm39)	missense	probably damaging	0.97
R5089:Prdm5	UTSW	6	65,833,074 (GRCm39)	missense	probably benign	0.01
R5138:Prdm5	UTSW	6	65,833,086 (GRCm39)	nonsense	probably null
R5735:Prdm5	UTSW	6	65,904,974 (GRCm39)	missense	possibly damaging	0.93
R6355:Prdm5	UTSW	6	65,860,578 (GRCm39)	missense	probably damaging	1.00
R6743:Prdm5	UTSW	6	65,860,635 (GRCm39)	missense	probably damaging	1.00
R6769:Prdm5	UTSW	6	65,839,920 (GRCm39)	missense	probably damaging	0.98
R7216:Prdm5	UTSW	6	65,904,967 (GRCm39)	nonsense	probably null
R7305:Prdm5	UTSW	6	65,808,244 (GRCm39)	missense	possibly damaging	0.83
R7510:Prdm5	UTSW	6	65,904,976 (GRCm39)	missense	probably damaging	0.97
R8270:Prdm5	UTSW	6	65,913,058 (GRCm39)	missense	probably damaging	1.00
R8529:Prdm5	UTSW	6	65,878,829 (GRCm39)	missense	probably damaging	1.00
R8856:Prdm5	UTSW	6	65,860,569 (GRCm39)	missense	possibly damaging	0.80
R9283:Prdm5	UTSW	6	65,858,060 (GRCm39)	missense	probably damaging	0.98
R9427:Prdm5	UTSW	6	65,771,321 (GRCm39)	missense	possibly damaging	0.65
R9477:Prdm5	UTSW	6	65,771,342 (GRCm39)	missense	possibly damaging	0.48
X0017:Prdm5	UTSW	6	65,846,246 (GRCm39)	missense	possibly damaging	0.94

Predicted Primers

PCR Primer
(F):5'- CTTAGACCCACTAGCACATACTTG -3'
(R):5'- AGATAGGCACATAAACACTGTCAG -3'

Sequencing Primer
(F):5'- CCACTAGCACATACTTGATAGAAGG -3'
(R):5'- GTCAGATCAATGAATCCTTTGTGGC -3'

Posted On

2014-08-25