Mutagenetix > Incidental Mutation

Incidental Mutation 'R4411:Prdm5'

327907

Institutional Source

Beutler Lab

Gene Symbol

Prdm5

Ensembl Gene

ENSMUSG00000029913

Gene Name

PR domain containing 5

Synonyms

6530401I24Rik, PFM2, E130112L17Rik, 4432417F03Rik

MMRRC Submission

041693-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4411 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

65755972-65913994 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 65878771 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Stop codon at position 108 (Y108*)

Ref Sequence

ENSEMBL: ENSMUSP00000079979 (fasta)

Gene Model

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

AlphaFold

Q9CXE0

Predicted Effect

probably null
Transcript: ENSMUST00000031973
AA Change: Y302*

SMART Domains

Protein: ENSMUSP00000031973
Gene: ENSMUSG00000029913
AA Change: Y302*

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 null
Transcript: ENSMUST00000031976
AA Change: Y486*

SMART Domains

Protein: ENSMUSP00000031976
Gene: ENSMUSG00000029913
AA Change: Y486*

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 null
Transcript: ENSMUST00000081219
AA Change: Y108*

SMART Domains

Protein: ENSMUSP00000079979
Gene: ENSMUSG00000029913
AA Change: Y108*

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

0.9754

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

95% (62/65)

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	T	C	11: 110,042,781 (GRCm39)	I423V	probably benign	Het
Abl2	T	C	1: 156,457,652 (GRCm39)	V306A	possibly damaging	Het
Adcy4	T	C	14: 56,006,900 (GRCm39)	Y1006C	probably damaging	Het
Adprhl1	T	C	8: 13,296,114 (GRCm39)	K144E	probably benign	Het
Arid5b	T	C	10: 67,932,519 (GRCm39)	R885G	probably damaging	Het
Atp9a	A	T	2: 168,503,853 (GRCm39)	V613E	probably damaging	Het
Atxn7l1	G	T	12: 33,244,886 (GRCm39)		probably benign	Het
Brd8	C	A	18: 34,756,497 (GRCm39)		probably benign	Het
Bsnd	C	T	4: 106,343,868 (GRCm39)	R146H	probably benign	Het
C4b	C	T	17: 34,947,838 (GRCm39)	R1659H	probably damaging	Het
Duox1	G	A	2: 122,168,115 (GRCm39)	R1080H	probably benign	Het
Eml2	T	C	7: 18,916,326 (GRCm39)		probably null	Het
Fbxo44	G	A	4: 148,238,065 (GRCm39)	R221C	probably damaging	Het
Frem1	T	C	4: 82,881,481 (GRCm39)	D166G	probably damaging	Het
Galnt5	T	C	2: 57,889,207 (GRCm39)	L269P	probably benign	Het
Gigyf2	A	G	1: 87,364,582 (GRCm39)	E954G	probably damaging	Het
Gpc6	T	C	14: 118,188,590 (GRCm39)	V408A	probably benign	Het
Hspg2	A	G	4: 137,289,535 (GRCm39)	T3832A	probably benign	Het
Ift88	A	G	14: 57,715,436 (GRCm39)	N493S	probably damaging	Het
Ighv1-76	A	T	12: 115,811,731 (GRCm39)	C41S	probably damaging	Het
Igkv12-46	G	A	6: 69,741,930 (GRCm39)	T16I	probably benign	Het
Igkv3-9	G	T	6: 70,565,547 (GRCm39)	V49F	probably damaging	Het
Isoc2b	A	T	7: 4,852,433 (GRCm39)		probably benign	Het
Lcp2	T	A	11: 34,037,173 (GRCm39)		probably benign	Het
Lmntd1	A	G	6: 145,373,003 (GRCm39)		probably null	Het
Mdm2	A	T	10: 117,545,694 (GRCm39)		probably null	Het
Mrgprx3-ps	T	C	7: 46,959,746 (GRCm39)		noncoding transcript	Het
Msh2	T	C	17: 88,025,032 (GRCm39)	S637P	probably damaging	Het
Myo5b	T	C	18: 74,831,345 (GRCm39)	F765S	possibly damaging	Het
Nav2	T	A	7: 49,047,857 (GRCm39)	N91K	probably benign	Het
Ndor1	G	A	2: 25,138,492 (GRCm39)	P363S	probably benign	Het
Npr3	G	C	15: 11,905,235 (GRCm39)	T164R	probably benign	Het
Pcdhb5	T	C	18: 37,455,050 (GRCm39)	S477P	possibly damaging	Het
Pde3b	GTGATGATGATGATGATGATGATGATG	GTGATGATGATGATGATGATGATG	7: 114,133,984 (GRCm39)		probably benign	Het
Pnpla7	G	A	2: 24,941,716 (GRCm39)	W13*	probably null	Het
Pnpla8	T	C	12: 44,330,225 (GRCm39)	V41A	probably benign	Het
Prdm2	A	T	4: 142,860,240 (GRCm39)	S1017T	probably benign	Het
Rab34	T	A	11: 78,079,592 (GRCm39)		probably null	Het
Skic3	A	G	13: 76,275,623 (GRCm39)	E410G	possibly damaging	Het
Smpd5	G	T	15: 76,179,112 (GRCm39)	R160L	possibly damaging	Het
Spmip10	A	G	18: 56,727,720 (GRCm39)	T65A	probably benign	Het
Srrm2	A	G	17: 24,029,442 (GRCm39)		probably benign	Het
Taf5	T	A	19: 47,059,453 (GRCm39)	V199D	probably damaging	Het
Tas2r114	C	T	6: 131,666,585 (GRCm39)	V148I	probably benign	Het
Tas2r136	C	A	6: 132,754,972 (GRCm39)	V52L	probably damaging	Het
Tnfrsf25	G	A	4: 152,202,843 (GRCm39)		probably benign	Het
Tpd52l1	T	C	10: 31,255,315 (GRCm39)	T11A	possibly damaging	Het
Trmt1l	G	A	1: 151,327,905 (GRCm39)	E472K	probably benign	Het
Ttc17	T	C	2: 94,173,098 (GRCm39)	K766E	probably damaging	Het
Ttn	C	T	2: 76,560,633 (GRCm39)	R29256Q	probably damaging	Het
Ttn	T	C	2: 76,572,414 (GRCm39)	I26160V	probably damaging	Het
Ubxn6	A	T	17: 56,376,303 (GRCm39)	V311E	probably damaging	Het
Usp2	T	C	9: 44,002,360 (GRCm39)	S351P	probably damaging	Het
Usp7	C	A	16: 8,526,778 (GRCm39)	D187Y	probably damaging	Het
Vmn1r115	C	T	7: 20,578,207 (GRCm39)	R235K	probably benign	Het
Vmn2r50	A	C	7: 9,784,235 (GRCm39)	F80V	probably damaging	Het
Vmn2r58	T	A	7: 41,511,360 (GRCm39)	K481M	possibly damaging	Het
Vmn2r86	A	G	10: 130,288,469 (GRCm39)	I344T	possibly damaging	Het
Zfp455	A	T	13: 67,355,389 (GRCm39)	N219I	probably 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
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
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'- TTGAAGGACATGCAGCAACCC -3'
(R):5'- AAAGTCAGGACACTTTGGGG -3'

Sequencing Primer
(F):5'- TTGGGCTCGAGGGCATAC -3'
(R):5'- AAGCTAGACATTGACATAACTTCAG -3'

Posted On

2015-07-07