Mutagenetix > Incidental Mutation

Incidental Mutation 'R1355:Prdm2'

156269

Institutional Source

Beutler Lab

Gene Symbol

Prdm2

Ensembl Gene

ENSMUSG00000057637

Gene Name

PR domain containing 2, with ZNF domain

Synonyms

KMT8, LOC381568, E330024L24Rik, Riz1, Riz, 4833427P12Rik

MMRRC Submission

039420-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1355 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

143107391-143212995 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 143131963 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 1586 (V1586I)

Ref Sequence

ENSEMBL: ENSMUSP00000101404 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000105778]

AlphaFold

A2A7B5

Predicted Effect

probably benign
Transcript: ENSMUST00000105778
AA Change: V1586I

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000101404
Gene: ENSMUSG00000057637
AA Change: V1586I

Domain	Start	End	E-Value	Type
SET	29	146	2.79e-21	SMART
coiled coil region	254	293	N/A	INTRINSIC
low complexity region	333	346	N/A	INTRINSIC
ZnF_C2H2	356	378	2.95e-3	SMART
ZnF_C2H2	386	408	4.79e-3	SMART
ZnF_C2H2	477	500	4.17e-3	SMART
low complexity region	517	528	N/A	INTRINSIC
low complexity region	653	669	N/A	INTRINSIC
low complexity region	682	697	N/A	INTRINSIC
low complexity region	726	744	N/A	INTRINSIC
low complexity region	868	877	N/A	INTRINSIC
low complexity region	931	951	N/A	INTRINSIC
low complexity region	954	992	N/A	INTRINSIC
low complexity region	1011	1032	N/A	INTRINSIC
low complexity region	1035	1080	N/A	INTRINSIC
ZnF_C2H2	1126	1148	3.52e-1	SMART
ZnF_C2H2	1154	1177	7.55e-1	SMART
ZnF_C2H2	1183	1206	4.72e-2	SMART
low complexity region	1239	1253	N/A	INTRINSIC
ZnF_C2H2	1324	1344	5.12e1	SMART
low complexity region	1406	1423	N/A	INTRINSIC
ZnF_C2H2	1446	1466	1.86e1	SMART
low complexity region	1475	1507	N/A	INTRINSIC
low complexity region	1551	1568	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197026

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.8%
20x: 91.4%

Validation Efficiency

100% (57/57)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene. Although the functions of this protein have not been fully characterized, it may (1) play a role in transcriptional regulation during neuronal differentiation and pathogenesis of retinoblastoma, (2) act as a transcriptional activator of the heme-oxygenase-1 gene, and (3) be a specific effector of estrogen action. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
PHENOTYPE: Homozygous null mice have shortened life spans, becoming moribund due to increased incidence of tumors. Mice had a broad spectrum of unusual tumors in multiple organs, with a high incidence of diffuse large B cell lymphomas. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb10	C	T	8: 123,962,052 (GRCm38)	G495D	probably damaging	Het
Ankrd52	A	G	10: 128,388,696 (GRCm38)	D781G	possibly damaging	Het
Arhgef5	T	A	6: 43,283,912 (GRCm38)	F1424I	probably damaging	Het
Atp10b	G	A	11: 43,151,655 (GRCm38)	W14*	probably null	Het
B4galnt4	T	C	7: 141,065,395 (GRCm38)	V259A	probably damaging	Het
Ccdc141	A	T	2: 77,030,601 (GRCm38)	I944N	probably damaging	Het
Ccdc146	A	T	5: 21,321,242 (GRCm38)	D224E	probably damaging	Het
Ccne1	A	G	7: 38,106,322 (GRCm38)	I43T	possibly damaging	Het
Cd226	T	A	18: 89,247,023 (GRCm38)	S29T	probably benign	Het
Cebpz	G	T	17: 78,935,324 (GRCm38)	D300E	probably benign	Het
Cryzl1	A	G	16: 91,692,658 (GRCm38)	V266A	possibly damaging	Het
Cyp2c68	A	G	19: 39,740,956 (GRCm38)	L29P	probably damaging	Het
Dennd3	A	C	15: 73,540,854 (GRCm38)		probably benign	Het
Dpy19l4	C	T	4: 11,303,371 (GRCm38)	W183*	probably null	Het
Eml6	T	G	11: 29,833,085 (GRCm38)	S599R	probably benign	Het
Erc1	A	T	6: 119,743,420 (GRCm38)	L440*	probably null	Het
Fam71e1	A	G	7: 44,496,691 (GRCm38)	K2E	possibly damaging	Het
Frem3	A	G	8: 80,690,702 (GRCm38)	Y2012C	probably damaging	Het
Gm10288	A	T	3: 146,838,993 (GRCm38)		noncoding transcript	Het
Gm1110	T	A	9: 26,883,761 (GRCm38)	K476N	probably benign	Het
Gm11937	A	T	11: 99,609,907 (GRCm38)	S95T	possibly damaging	Het
Hist1h2bl	T	A	13: 21,715,857 (GRCm38)	Q96L	probably damaging	Het
Hs6st1	T	A	1: 36,103,576 (GRCm38)	H197Q	probably damaging	Het
Ism1	A	T	2: 139,732,074 (GRCm38)	I115F	possibly damaging	Het
Itgb8	C	T	12: 119,171,003 (GRCm38)	G443E	probably benign	Het
Kalrn	T	A	16: 33,975,584 (GRCm38)	I1274F	possibly damaging	Het
Lrrcc1	G	T	3: 14,548,114 (GRCm38)	V299L	probably benign	Het
Mettl5	A	T	2: 69,881,420 (GRCm38)		probably null	Het
Nlrp2	G	T	7: 5,327,491 (GRCm38)	N635K	possibly damaging	Het
Olfr140	G	A	2: 90,051,613 (GRCm38)	T237I	probably benign	Het
Olfr1466	T	A	19: 13,342,518 (GRCm38)	Y253*	probably null	Het
Olfr1537	G	C	9: 39,238,251 (GRCm38)	P58A	probably benign	Het
Olfr198	A	G	16: 59,201,680 (GRCm38)	S249P	probably damaging	Het
Plxna1	A	G	6: 89,320,766 (GRCm38)		probably benign	Het
Ppp4r1	A	T	17: 65,840,987 (GRCm38)	E924D	probably benign	Het
Pros1	A	G	16: 62,919,558 (GRCm38)	K457E	probably benign	Het
Rer1	T	A	4: 155,075,624 (GRCm38)	M156L	probably benign	Het
Rgs16	A	T	1: 153,743,668 (GRCm38)	K140M	probably damaging	Het
Rgsl1	A	G	1: 153,807,761 (GRCm38)	M1T	probably null	Het
Setdb2	T	A	14: 59,417,441 (GRCm38)	K333N	probably damaging	Het
Sgo2a	A	G	1: 58,017,965 (GRCm38)	T1103A	possibly damaging	Het
Sik3	C	T	9: 46,195,872 (GRCm38)		probably benign	Het
Slc44a3	C	A	3: 121,531,671 (GRCm38)	G47V	probably damaging	Het
Snrpd1	G	A	18: 10,627,818 (GRCm38)	G103D	probably benign	Het
Soga3	A	T	10: 29,147,322 (GRCm38)	T222S	probably benign	Het
Sspo	T	A	6: 48,448,626 (GRCm38)	S60R	probably benign	Het
Susd1	C	T	4: 59,424,114 (GRCm38)	C37Y	possibly damaging	Het
Tiam1	A	T	16: 89,898,221 (GRCm38)	I116N	probably benign	Het
Ttc3	A	G	16: 94,418,637 (GRCm38)	S492G	possibly damaging	Het
Uckl1	G	T	2: 181,573,376 (GRCm38)	T213K	probably damaging	Het
Usp38	T	C	8: 80,985,033 (GRCm38)	E791G	possibly damaging	Het
Vps13b	C	T	15: 35,422,454 (GRCm38)	R187C	probably damaging	Het
Vwa3a	A	G	7: 120,784,111 (GRCm38)	Y645C	probably damaging	Het
Wasf3	T	C	5: 146,470,208 (GRCm38)		probably benign	Het

Other mutations in Prdm2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00530:Prdm2	APN	4	143,133,759 (GRCm38)	missense	probably damaging	0.99
IGL00843:Prdm2	APN	4	143,134,314 (GRCm38)	missense	probably damaging	1.00
IGL01419:Prdm2	APN	4	143,133,648 (GRCm38)	missense	probably damaging	0.99
IGL01662:Prdm2	APN	4	143,133,568 (GRCm38)	missense	possibly damaging	0.73
IGL01892:Prdm2	APN	4	143,134,404 (GRCm38)	missense	probably damaging	1.00
IGL02104:Prdm2	APN	4	143,133,427 (GRCm38)	missense	probably benign	0.01
IGL02208:Prdm2	APN	4	143,135,743 (GRCm38)	missense	probably benign	0.01
IGL02260:Prdm2	APN	4	143,134,587 (GRCm38)	missense	probably damaging	1.00
IGL02479:Prdm2	APN	4	143,134,929 (GRCm38)	missense	probably damaging	1.00
IGL02943:Prdm2	APN	4	143,131,972 (GRCm38)	missense	probably benign
IGL02972:Prdm2	APN	4	143,132,166 (GRCm38)	missense	probably benign
IGL03038:Prdm2	APN	4	143,134,001 (GRCm38)	missense	probably damaging	1.00
IGL03399:Prdm2	APN	4	143,135,088 (GRCm38)	missense	probably benign	0.07
G1patch:Prdm2	UTSW	4	143,132,901 (GRCm38)	missense	possibly damaging	0.96
PIT4677001:Prdm2	UTSW	4	143,135,078 (GRCm38)	missense	probably damaging	1.00
R0088:Prdm2	UTSW	4	143,134,954 (GRCm38)	missense	possibly damaging	0.86
R0153:Prdm2	UTSW	4	143,133,768 (GRCm38)	missense	possibly damaging	0.93
R0320:Prdm2	UTSW	4	143,179,351 (GRCm38)	missense	probably damaging	1.00
R0384:Prdm2	UTSW	4	143,135,688 (GRCm38)	missense	probably benign	0.01
R0400:Prdm2	UTSW	4	143,111,670 (GRCm38)	missense	probably benign
R0658:Prdm2	UTSW	4	143,135,265 (GRCm38)	missense	probably damaging	1.00
R0850:Prdm2	UTSW	4	143,132,203 (GRCm38)	missense	possibly damaging	0.53
R1118:Prdm2	UTSW	4	143,132,383 (GRCm38)	missense	possibly damaging	0.52
R1519:Prdm2	UTSW	4	143,135,583 (GRCm38)	missense	probably damaging	1.00
R1936:Prdm2	UTSW	4	143,134,462 (GRCm38)	missense	probably benign	0.00
R1987:Prdm2	UTSW	4	143,132,509 (GRCm38)	missense	possibly damaging	0.73
R2006:Prdm2	UTSW	4	143,131,877 (GRCm38)	missense	possibly damaging	0.73
R2008:Prdm2	UTSW	4	143,134,947 (GRCm38)	missense	probably damaging	1.00
R2030:Prdm2	UTSW	4	143,132,764 (GRCm38)	missense	possibly damaging	0.53
R2112:Prdm2	UTSW	4	143,131,936 (GRCm38)	missense	probably benign
R2221:Prdm2	UTSW	4	143,134,899 (GRCm38)	missense	possibly damaging	0.58
R2223:Prdm2	UTSW	4	143,134,899 (GRCm38)	missense	possibly damaging	0.58
R2426:Prdm2	UTSW	4	143,111,750 (GRCm38)	nonsense	probably null
R2430:Prdm2	UTSW	4	143,133,163 (GRCm38)	missense	possibly damaging	0.73
R2484:Prdm2	UTSW	4	143,135,206 (GRCm38)	missense	probably damaging	1.00
R3735:Prdm2	UTSW	4	143,134,359 (GRCm38)	missense	probably damaging	1.00
R3944:Prdm2	UTSW	4	143,131,815 (GRCm38)	missense	possibly damaging	0.53
R4209:Prdm2	UTSW	4	143,134,437 (GRCm38)	missense	probably damaging	1.00
R4411:Prdm2	UTSW	4	143,133,670 (GRCm38)	missense	probably benign	0.18
R4647:Prdm2	UTSW	4	143,132,955 (GRCm38)	missense	possibly damaging	0.85
R4898:Prdm2	UTSW	4	143,134,191 (GRCm38)	missense	probably damaging	1.00
R5032:Prdm2	UTSW	4	143,179,367 (GRCm38)	nonsense	probably null
R5181:Prdm2	UTSW	4	143,134,966 (GRCm38)	missense	probably benign	0.35
R5513:Prdm2	UTSW	4	143,135,893 (GRCm38)	small deletion	probably benign
R5539:Prdm2	UTSW	4	143,132,694 (GRCm38)	missense	possibly damaging	0.53
R5563:Prdm2	UTSW	4	143,134,630 (GRCm38)	missense	probably benign	0.09
R5618:Prdm2	UTSW	4	143,133,537 (GRCm38)	missense	probably benign	0.00
R5900:Prdm2	UTSW	4	143,134,720 (GRCm38)	missense	probably damaging	1.00
R5990:Prdm2	UTSW	4	143,170,113 (GRCm38)	missense	probably damaging	1.00
R6148:Prdm2	UTSW	4	143,132,907 (GRCm38)	missense	probably benign	0.33
R6166:Prdm2	UTSW	4	143,134,736 (GRCm38)	missense	probably damaging	0.99
R6223:Prdm2	UTSW	4	143,142,207 (GRCm38)	missense	probably benign	0.41
R6530:Prdm2	UTSW	4	143,134,047 (GRCm38)	missense	probably benign	0.05
R6631:Prdm2	UTSW	4	143,134,884 (GRCm38)	missense	probably benign	0.05
R6725:Prdm2	UTSW	4	143,132,901 (GRCm38)	missense	possibly damaging	0.96
R6847:Prdm2	UTSW	4	143,132,950 (GRCm38)	missense	probably benign	0.18
R7193:Prdm2	UTSW	4	143,180,894 (GRCm38)	missense	probably damaging	1.00
R7238:Prdm2	UTSW	4	143,135,821 (GRCm38)	missense	probably benign	0.35
R7292:Prdm2	UTSW	4	143,132,901 (GRCm38)	missense	possibly damaging	0.96
R7417:Prdm2	UTSW	4	143,179,299 (GRCm38)	missense	probably damaging	1.00
R7748:Prdm2	UTSW	4	143,135,889 (GRCm38)	missense	possibly damaging	0.89
R7885:Prdm2	UTSW	4	143,134,570 (GRCm38)	missense	probably benign	0.41
R7936:Prdm2	UTSW	4	143,135,864 (GRCm38)	missense	probably damaging	0.99
R7976:Prdm2	UTSW	4	143,133,242 (GRCm38)	nonsense	probably null
R8124:Prdm2	UTSW	4	143,135,265 (GRCm38)	missense	probably damaging	1.00
R8150:Prdm2	UTSW	4	143,132,733 (GRCm38)	missense	possibly damaging	0.73
R8156:Prdm2	UTSW	4	143,134,768 (GRCm38)	missense	probably benign	0.01
R8178:Prdm2	UTSW	4	143,132,448 (GRCm38)	missense	probably benign	0.33
R8235:Prdm2	UTSW	4	143,132,467 (GRCm38)	nonsense	probably null
R8404:Prdm2	UTSW	4	143,135,014 (GRCm38)	missense	probably damaging	0.98
R8498:Prdm2	UTSW	4	143,180,897 (GRCm38)	missense	probably damaging	1.00
R8502:Prdm2	UTSW	4	143,135,014 (GRCm38)	missense	probably damaging	0.98
R8688:Prdm2	UTSW	4	143,111,740 (GRCm38)	missense	probably benign
R8732:Prdm2	UTSW	4	143,136,010 (GRCm38)	missense	probably benign	0.00
R8796:Prdm2	UTSW	4	143,133,447 (GRCm38)	missense	probably benign	0.33
R8874:Prdm2	UTSW	4	143,133,215 (GRCm38)	missense	possibly damaging	0.70
R8887:Prdm2	UTSW	4	143,134,201 (GRCm38)	missense	probably damaging	1.00
R9119:Prdm2	UTSW	4	143,131,879 (GRCm38)	nonsense	probably null
R9139:Prdm2	UTSW	4	143,132,182 (GRCm38)	missense	probably benign	0.03
R9165:Prdm2	UTSW	4	143,132,104 (GRCm38)	missense	possibly damaging	0.73
R9342:Prdm2	UTSW	4	143,134,908 (GRCm38)	missense	probably damaging	1.00
R9518:Prdm2	UTSW	4	143,134,009 (GRCm38)	missense	possibly damaging	0.94
R9546:Prdm2	UTSW	4	143,134,991 (GRCm38)	missense	probably damaging	1.00
R9547:Prdm2	UTSW	4	143,134,991 (GRCm38)	missense	probably damaging	1.00
R9680:Prdm2	UTSW	4	143,132,509 (GRCm38)	missense	possibly damaging	0.73
R9730:Prdm2	UTSW	4	143,132,089 (GRCm38)	missense	possibly damaging	0.73
X0017:Prdm2	UTSW	4	143,134,707 (GRCm38)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TGCCACAAGATTATGCCAGTGCC -3'
(R):5'- CACCGCAGATACGGAGATCAAGATG -3'

Sequencing Primer
(F):5'- AAGATTATGCCAGTGCCACTCTG -3'
(R):5'- CACCCTTGGGCAAGACC -3'

Posted On

2014-02-11