Mutagenetix > Incidental Mutation

Incidental Mutation 'R7510:Prdm5'

582024

Institutional Source

Beutler Lab

Gene Symbol

Prdm5

Ensembl Gene

ENSMUSG00000029913

Gene Name

PR domain containing 5

Synonyms

6530401I24Rik, PFM2, E130112L17Rik, 4432417F03Rik

MMRRC Submission

045583-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7510 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

65755972-65913994 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 65904976 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Tyrosine at position 536 (H536Y)

Ref Sequence

ENSEMBL: ENSMUSP00000031976 (fasta)

Gene Model

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

AlphaFold

Q9CXE0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000031973
AA Change: H352Y

PolyPhen 2 Score 0.490 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000031973
Gene: ENSMUSG00000029913
AA Change: H352Y

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: H536Y

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000031976
Gene: ENSMUSG00000029913
AA Change: H536Y

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: H158Y

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000079979
Gene: ENSMUSG00000029913
AA Change: H158Y

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

Meta Mutation Damage Score

0.8166

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.0%

Validation Efficiency

97% (65/67)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Atp2b1	C	T	10: 98,829,758 (GRCm39)	R320C	probably benign	Het
Bend4	A	G	5: 67,584,727 (GRCm39)	F66L	unknown	Het
Brca2	T	C	5: 150,460,156 (GRCm39)	V477A	possibly damaging	Het
Brms1l	A	T	12: 55,892,107 (GRCm39)	K134*	probably null	Het
Catsper1	A	T	19: 5,389,578 (GRCm39)	T498S	probably benign	Het
Ccdc177	C	A	12: 80,804,457 (GRCm39)	V606L	unknown	Het
D030056L22Rik	G	T	19: 18,690,853 (GRCm39)	A56S	possibly damaging	Het
Disp1	T	C	1: 182,869,975 (GRCm39)	N815S	probably damaging	Het
Dsc2	C	T	18: 20,165,331 (GRCm39)	G881R	possibly damaging	Het
Fancf	A	G	7: 51,511,953 (GRCm39)	V17A	probably damaging	Het
Fastkd2	T	A	1: 63,776,948 (GRCm39)	H361Q	possibly damaging	Het
Furin	A	G	7: 80,043,333 (GRCm39)	S293P	probably damaging	Het
Ghsr	A	T	3: 27,426,523 (GRCm39)	D193V	probably benign	Het
Gm14403	T	A	2: 177,200,403 (GRCm39)	N116K	probably benign	Het
Gpr31b	A	G	17: 13,270,557 (GRCm39)	L204P	probably damaging	Het
Hexim1	A	G	11: 103,008,067 (GRCm39)	E107G	probably benign	Het
Hspa14	T	C	2: 3,499,159 (GRCm39)	S212G	probably benign	Het
Il18r1	T	A	1: 40,514,035 (GRCm39)	H80Q	probably benign	Het
Itpr3	A	G	17: 27,308,013 (GRCm39)	T267A	probably damaging	Het
Kidins220	T	A	12: 25,042,268 (GRCm39)	H146Q	possibly damaging	Het
Larp4	T	C	15: 99,891,258 (GRCm39)	F228L	probably benign	Het
Ltbp1	T	A	17: 75,659,712 (GRCm39)	V1288E	probably damaging	Het
Madd	T	C	2: 91,008,321 (GRCm39)	T194A	possibly damaging	Het
Mlana	G	A	19: 29,682,072 (GRCm39)	G42S	probably benign	Het
Mlxipl	A	G	5: 135,161,972 (GRCm39)	E548G	possibly damaging	Het
Mmab	A	T	5: 114,573,283 (GRCm39)	C228S	probably benign	Het
Mmp1a	TG	TGG	9: 7,465,083 (GRCm38)		probably null	Het
Nrf1	C	T	6: 30,151,633 (GRCm39)	T490I	possibly damaging	Het
Numbl	A	G	7: 26,971,412 (GRCm39)		probably null	Het
Or12e13	T	A	2: 87,663,872 (GRCm39)	I163K	probably damaging	Het
Or13c7	A	G	4: 43,854,482 (GRCm39)	T58A	probably benign	Het
Or5bw2	C	T	7: 6,572,960 (GRCm39)		probably benign	Het
Or5v1b	T	A	17: 37,841,480 (GRCm39)	I204N	probably damaging	Het
Or6c3b	G	T	10: 129,527,789 (GRCm39)	N40K	probably damaging	Het
Or9g8	T	A	2: 85,607,153 (GRCm39)	V75D	probably damaging	Het
Papln	G	A	12: 83,818,947 (GRCm39)	D96N	probably damaging	Het
Pcdhb14	T	C	18: 37,582,645 (GRCm39)	Y584H	probably damaging	Het
Pde7b	T	C	10: 20,288,761 (GRCm39)	D310G	possibly damaging	Het
Plin5	T	A	17: 56,420,975 (GRCm39)	H230L	probably damaging	Het
Ppp1r13l	A	C	7: 19,102,726 (GRCm39)	E47A	possibly damaging	Het
Prickle2	T	C	6: 92,353,451 (GRCm39)	R728G	possibly damaging	Het
Prkca	A	T	11: 107,874,820 (GRCm39)	V374E	possibly damaging	Het
Prss3	A	T	6: 41,352,044 (GRCm39)	L73*	probably null	Het
Prss51	G	A	14: 64,333,489 (GRCm39)	D33N	probably damaging	Het
Rfwd3	A	G	8: 112,006,659 (GRCm39)	V479A	probably damaging	Het
Rpl36a-ps1	G	A	14: 99,231,666 (GRCm39)	T24I	probably benign	Het
Rps6ka5	T	C	12: 100,582,327 (GRCm39)	I182V	possibly damaging	Het
Saa2	T	A	7: 46,402,933 (GRCm39)	D61E	probably damaging	Het
Samd3	A	T	10: 26,106,006 (GRCm39)	I22F	probably benign	Het
Sap130	C	T	18: 31,800,057 (GRCm39)	P403L	probably damaging	Het
Sap130	A	G	18: 31,844,268 (GRCm39)	T813A	probably damaging	Het
Scfd2	A	G	5: 74,372,988 (GRCm39)	F629S	probably damaging	Het
Sec61a1	A	T	6: 88,489,585 (GRCm39)	F119I	probably benign	Het
Serpinb9	T	A	13: 33,194,768 (GRCm39)	F175I	probably damaging	Het
Slc12a3	G	T	8: 95,092,477 (GRCm39)	C966F	probably damaging	Het
Sptbn4	A	G	7: 27,127,693 (GRCm39)	V169A	probably benign	Het
Synj1	A	G	16: 90,735,565 (GRCm39)	S1463P	probably benign	Het
Tfec	T	A	6: 16,835,232 (GRCm39)	H182L	probably benign	Het
Tigd5	T	C	15: 75,782,268 (GRCm39)	V210A	probably benign	Het
Tssc4	G	A	7: 142,623,718 (GRCm39)	E9K	possibly damaging	Het
Txk	C	G	5: 72,893,726 (GRCm39)	C18S	unknown	Het
Uaca	G	A	9: 60,757,487 (GRCm39)		probably null	Het
Vmn2r1	A	C	3: 63,993,922 (GRCm39)	K89N	probably damaging	Het
Zfp160	G	A	17: 21,246,655 (GRCm39)	E402K	probably benign	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
R1997: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
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'- AGCAGCCACTCACTTTTCTGTG -3'
(R):5'- GCTGCTAGAAAACCATGATGAGTAG -3'

Sequencing Primer
(F):5'- AATCAGCCATCTTTCCATGGAGG -3'
(R):5'- ACCATGATGAGTAGAATATGAATGC -3'

Posted On

2019-10-17