Mutagenetix > Incidental Mutation

Incidental Mutation 'R2019:Prdm5'

223620

Institutional Source

Beutler Lab

Gene Symbol

Prdm5

Ensembl Gene

ENSMUSG00000029913

Gene Name

PR domain containing 5

Synonyms

6530401I24Rik, PFM2, E130112L17Rik, 4432417F03Rik

MMRRC Submission

040028-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2019 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

65755972-65913994 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 65808340 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 95 (N95K)

Ref Sequence

ENSEMBL: ENSMUSP00000031973 (fasta)

Gene Model

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

AlphaFold

Q9CXE0

Predicted Effect

probably damaging
Transcript: ENSMUST00000031973
AA Change: N95K

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000031973
Gene: ENSMUSG00000029913
AA Change: N95K

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: N95K

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000031976
Gene: ENSMUSG00000029913
AA Change: N95K

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

possibly damaging
Transcript: ENSMUST00000081219
AA Change: N67K

PolyPhen 2 Score 0.719 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000079979
Gene: ENSMUSG00000029913
AA Change: N67K

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 damaging
Transcript: ENSMUST00000172638
AA Change: N95K

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000133423
Gene: ENSMUSG00000029913
AA Change: N95K

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: ENSMUST00000173538

Meta Mutation Damage Score

0.5429

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.0%
20x: 94.4%

Validation Efficiency

100% (71/71)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610028H24Rik	C	A	10: 76,293,899 (GRCm39)	F252L	possibly damaging	Het
Abcc9	G	A	6: 142,621,160 (GRCm39)	L527F	probably damaging	Het
Abi3bp	A	G	16: 56,498,159 (GRCm39)	T918A	probably damaging	Het
Acp3	C	T	9: 104,201,901 (GRCm39)	G81R	probably damaging	Het
Acss3	C	T	10: 106,772,068 (GRCm39)	S669N	probably benign	Het
Akt1	T	C	12: 112,626,059 (GRCm39)	N71S	probably damaging	Het
Amz1	G	T	5: 140,737,719 (GRCm39)	M326I	probably benign	Het
Ankrd36	A	G	11: 5,639,140 (GRCm39)	I1351V	probably benign	Het
Art2b	T	C	7: 101,229,194 (GRCm39)	D235G	probably benign	Het
Ccdc141	A	C	2: 76,841,909 (GRCm39)	I1507M	probably damaging	Het
Dck	A	G	5: 88,921,943 (GRCm39)	Y135C	probably damaging	Het
Dmbt1	T	G	7: 130,712,718 (GRCm39)	I1563S	possibly damaging	Het
Dnttip2	T	C	3: 122,074,393 (GRCm39)	V610A	possibly damaging	Het
Efhb	A	G	17: 53,708,505 (GRCm39)	S722P	probably damaging	Het
Emx2	A	G	19: 59,447,771 (GRCm39)	S42G	probably benign	Het
Ermard	C	T	17: 15,273,527 (GRCm39)	R371C	probably damaging	Het
Fat1	T	G	8: 45,476,783 (GRCm39)	I1943S	probably damaging	Het
Fignl1	T	C	11: 11,752,054 (GRCm39)	K334E	probably damaging	Het
Fmn1	A	C	2: 113,194,825 (GRCm39)	K175T	unknown	Het
Gm7247	A	T	14: 51,602,804 (GRCm39)	M47L	possibly damaging	Het
Gpalpp1	A	T	14: 76,348,131 (GRCm39)		probably null	Het
Hc	A	C	2: 34,903,540 (GRCm39)	F1038C	probably damaging	Het
Ifngr1	A	T	10: 19,467,861 (GRCm39)	M10L	probably damaging	Het
Irx5	T	G	8: 93,084,992 (GRCm39)	Y61D	probably damaging	Het
Itgax	A	G	7: 127,747,698 (GRCm39)	H1038R	probably benign	Het
Jag1	C	T	2: 136,926,599 (GRCm39)	E982K	probably benign	Het
Klhdc9	T	C	1: 171,186,509 (GRCm39)	D309G	probably damaging	Het
Lamp3	A	T	16: 19,519,961 (GRCm39)	M74K	probably benign	Het
Lrpprc	A	T	17: 85,059,759 (GRCm39)	L685Q	possibly damaging	Het
Magel2	G	A	7: 62,028,844 (GRCm39)	V583I	unknown	Het
Mgat5b	A	G	11: 116,838,174 (GRCm39)	Y271C	probably benign	Het
Mtmr6	T	C	14: 60,536,441 (GRCm39)	M557T	probably benign	Het
Myo16	T	C	8: 10,426,260 (GRCm39)	L339P	probably benign	Het
Neb	G	T	2: 52,122,288 (GRCm39)	Y580*	probably null	Het
Npat	A	G	9: 53,473,791 (GRCm39)	K528E	probably benign	Het
Or1j4	A	T	2: 36,740,418 (GRCm39)	Y120F	possibly damaging	Het
Or4a72	A	G	2: 89,405,737 (GRCm39)	V111A	probably damaging	Het
Or5m3	A	T	2: 85,838,567 (GRCm39)	Y149F	probably damaging	Het
Parp8	G	A	13: 117,004,968 (GRCm39)		probably benign	Het
Phf3	G	A	1: 30,850,928 (GRCm39)	T1142M	probably damaging	Het
Phospho1	G	A	11: 95,721,932 (GRCm39)	V201M	probably damaging	Het
Piezo1	A	G	8: 123,209,451 (GRCm39)	F2371L	probably benign	Het
Pitpnm1	T	C	19: 4,163,641 (GRCm39)	S1209P	probably damaging	Het
Pkd1	T	A	17: 24,787,658 (GRCm39)	C20*	probably null	Het
Prkx	T	C	X: 76,809,010 (GRCm39)	D270G	probably damaging	Het
Ptgis	A	G	2: 167,050,199 (GRCm39)	V310A	probably damaging	Het
Ptgis	G	A	2: 167,056,730 (GRCm39)	Q286*	probably null	Het
Rpf1	T	A	3: 146,226,976 (GRCm39)	N59I	probably damaging	Het
Rpl3l	A	C	17: 24,954,490 (GRCm39)		probably benign	Het
Ryr2	C	T	13: 11,866,074 (GRCm39)	G292D	possibly damaging	Het
Ryr3	G	T	2: 112,611,410 (GRCm39)	N2257K	probably benign	Het
Sla	T	C	15: 66,654,404 (GRCm39)	Y278C	probably damaging	Het
Slc4a10	A	T	2: 62,064,725 (GRCm39)	D193V	probably damaging	Het
Spire2	T	C	8: 124,059,657 (GRCm39)	C52R	probably damaging	Het
Tada2b	T	C	5: 36,641,250 (GRCm39)	Y51C	probably damaging	Het
Tarbp1	C	T	8: 127,154,853 (GRCm39)	V1424I	probably damaging	Het
Tbpl1	T	A	10: 22,583,576 (GRCm39)	E131D	probably damaging	Het
Tgfbrap1	A	G	1: 43,093,677 (GRCm39)		probably null	Het
Tmem116	A	G	5: 121,627,317 (GRCm39)	I151M	possibly damaging	Het
Tmem30a	T	C	9: 79,681,500 (GRCm39)	D223G	probably damaging	Het
Trim13	T	A	14: 61,842,335 (GRCm39)	C117*	probably null	Het
Ttn	C	G	2: 76,585,676 (GRCm39)	D21987H	probably damaging	Het
Txnrd1	G	A	10: 82,713,207 (GRCm39)	V90I	probably benign	Het
Unc79	G	A	12: 103,137,830 (GRCm39)		probably null	Het
Upp1	A	T	11: 9,083,240 (GRCm39)	M111L	possibly damaging	Het
Vmn2r79	G	T	7: 86,651,634 (GRCm39)	L344F	probably benign	Het
Vps39	T	C	2: 120,173,708 (GRCm39)	Y147C	probably damaging	Het
Wdr59	A	G	8: 112,193,425 (GRCm39)	Y666H	probably damaging	Het
Wdr95	A	G	5: 149,497,613 (GRCm39)		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
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'- GGCTTCTGTAGACATAAGTTTAAGC -3'
(R):5'- GCGTTTTCCTGCATATGCCG -3'

Sequencing Primer
(F):5'- GACATAAGTTTAAGCCATGAGTGTTG -3'
(R):5'- GCATATGCCGACTACATGATTTC -3'

Posted On

2014-08-25