Mutagenetix > Incidental Mutation

Incidental Mutation 'R7570:Prdm9'

585762

Institutional Source

Beutler Lab

Gene Symbol

Prdm9

Ensembl Gene

ENSMUSG00000051977

Gene Name

PR domain containing 9

Synonyms

Meisetz, repro7, Dsbc1, Rcr1, G1-419-29

MMRRC Submission

045631-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.351) question?

Stock #

R7570 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

15763341-15784616 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 15775914 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 179 (N179S)

Ref Sequence

ENSEMBL: ENSMUSP00000131871 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000147532] [ENSMUST00000167994]

AlphaFold

Q96EQ9

Predicted Effect

probably benign
Transcript: ENSMUST00000147532
AA Change: N54S

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977
AA Change: N54S

Domain	Start	End	E-Value	Type
Pfam:SSXRD	49	81	1.8e-19	PFAM
SET	123	243	2.56e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000167994
AA Change: N179S

PolyPhen 2 Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: N179S

Domain	Start	End	E-Value	Type
KRAB	30	89	5.54e-8	SMART
Pfam:SSXRD	175	205	1.5e-20	PFAM
SET	248	368	2.56e-2	SMART
ZnF_C2H2	392	415	3.29e-1	SMART
ZnF_C2H2	516	535	4.74e1	SMART
ZnF_C2H2	541	563	9.73e-4	SMART
ZnF_C2H2	569	591	1.3e-4	SMART
ZnF_C2H2	597	619	1.3e-4	SMART
ZnF_C2H2	625	647	4.24e-4	SMART
ZnF_C2H2	653	675	4.24e-4	SMART
ZnF_C2H2	681	703	1.95e-3	SMART
ZnF_C2H2	709	731	5.99e-4	SMART
ZnF_C2H2	737	759	1.95e-3	SMART
ZnF_C2H2	765	787	1.95e-3	SMART
ZnF_C2H2	793	815	1.3e-4	SMART
ZnF_C2H2	821	843	1.6e-4	SMART

Meta Mutation Damage Score

0.0846

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

98% (104/106)

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 zinc finger protein with histone methyltransferase activity that catalyzes histone H3 lysine 4 trimethylation (H3K4me3) during meiotic prophase. This protein contains multiple domains, including a Kruppel-associated box (KRAB) domain, an SSX repression domain (SSXRD), a PRD1-BF1 and RIZ homologous region, a subclass of SET (PR/SET) domain, and a tandem array of C2H2 zinc fingers. The zinc finger array recognizes a short sequence motif, leading to local H3K4me3, and meiotic recombination hotspot activity. The observed allelic variation alters the DNA-binding sequence specificity of the protein, resulting in distinct meiotic recombination hotspots amongst individuals and populations. Multiple alternate alleles of this gene have been described. [provided by RefSeq, Jul 2015]
PHENOTYPE: Mice homozygous for a knock-out allele show decreased oocyte number, azoospermia, and sterility in both sexes due to severe impairment of the double-stranded break repair pathway, deficient pairing of homologous chromosomes, and impaired sex body formation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 106 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	C	T	6: 91,911,591 (GRCm39)	T613I	probably benign	Het
Ajuba	T	C	14: 54,813,859 (GRCm39)	E288G	probably damaging	Het
Ankrd12	C	T	17: 66,292,355 (GRCm39)	R1026K	probably benign	Het
Apol7b	T	C	15: 77,307,674 (GRCm39)	T274A	probably benign	Het
Arid4a	A	T	12: 71,109,916 (GRCm39)	R86*	probably null	Het
Asnsd1	C	T	1: 53,387,417 (GRCm39)	G70D	probably damaging	Het
Atg4c	T	A	4: 99,116,797 (GRCm39)	V313D	possibly damaging	Het
Atp13a5	A	C	16: 29,085,715 (GRCm39)	C885G	probably damaging	Het
Bpifb9a	A	T	2: 154,104,183 (GRCm39)	I209F	possibly damaging	Het
Bsn	T	C	9: 107,990,742 (GRCm39)	D1670G	probably damaging	Het
Cct8	T	A	16: 87,288,210 (GRCm39)	I121F	probably benign	Het
Cd209a	T	G	8: 3,794,151 (GRCm39)	D217A	probably damaging	Het
Cdk19	C	T	10: 40,353,954 (GRCm39)	S456L	possibly damaging	Het
Chd9	C	T	8: 91,721,208 (GRCm39)	H999Y	unknown	Het
Col5a1	G	A	2: 27,841,395 (GRCm39)	V339M	unknown	Het
Cr2	G	A	1: 194,851,648 (GRCm39)	R115*	probably null	Het
Cyb561	A	T	11: 105,828,470 (GRCm39)	F62I	probably damaging	Het
Cyp2c38	A	T	19: 39,393,187 (GRCm39)	N293K	possibly damaging	Het
Cyp2c69	A	T	19: 39,848,342 (GRCm39)	D293E	probably damaging	Het
Dcbld2	T	A	16: 58,244,932 (GRCm39)	C69S	possibly damaging	Het
Dcdc2a	T	C	13: 25,303,356 (GRCm39)	S296P	probably benign	Het
Dmxl1	T	A	18: 50,027,024 (GRCm39)	I2044K	possibly damaging	Het
Dnah5	A	G	15: 28,347,098 (GRCm39)	D2527G	probably damaging	Het
Dnah6	T	C	6: 73,126,413 (GRCm39)	T1305A	probably benign	Het
Dnajc9	A	G	14: 20,438,712 (GRCm39)	V47A	probably benign	Het
Dnmt3b	A	G	2: 153,518,619 (GRCm39)	Y594C	probably damaging	Het
Dph7	A	G	2: 24,855,642 (GRCm39)	D147G	probably damaging	Het
Drap1	T	C	19: 5,473,380 (GRCm39)	H164R	possibly damaging	Het
Dsg3	T	A	18: 20,660,837 (GRCm39)	V392E	possibly damaging	Het
Dxo	A	G	17: 35,056,616 (GRCm39)	D81G	probably benign	Het
E230025N22Rik	G	T	18: 36,828,645 (GRCm39)	T11K	probably benign	Het
Esyt1	A	G	10: 128,354,801 (GRCm39)	V533A	possibly damaging	Het
Etv3	T	A	3: 87,443,338 (GRCm39)	C307*	probably null	Het
Fam114a1	T	A	5: 65,187,402 (GRCm39)		probably null	Het
Fam3c	T	A	6: 22,326,404 (GRCm39)		probably benign	Het
Fbn1	G	T	2: 125,239,772 (GRCm39)	T305K	probably benign	Het
Ggt1	A	T	10: 75,421,428 (GRCm39)	I484F	probably damaging	Het
Gpatch1	T	C	7: 34,993,237 (GRCm39)	D536G	probably damaging	Het
Gpx4	T	C	10: 79,890,875 (GRCm39)	I189T	probably damaging	Het
Gsr	T	A	8: 34,159,193 (GRCm39)	C85S	probably damaging	Het
Gsta5	A	T	9: 78,211,751 (GRCm39)	D171V	possibly damaging	Het
Havcr1	T	A	11: 46,661,369 (GRCm39)		probably null	Het
Heatr4	T	C	12: 84,026,418 (GRCm39)	T280A	probably benign	Het
Hmcn2	A	T	2: 31,313,923 (GRCm39)	E3532D	probably benign	Het
Hnrnpc	T	C	14: 52,312,556 (GRCm39)	N308S	possibly damaging	Het
Ighv8-9	A	G	12: 115,432,358 (GRCm39)	V13A	probably benign	Het
Itgb2l	A	T	16: 96,227,439 (GRCm39)	F535I	probably benign	Het
Kdm5a	T	G	6: 120,404,803 (GRCm39)	D1348E	probably damaging	Het
Kndc1	CT	C	7: 139,503,691 (GRCm39)		probably null	Het
Ky	A	G	9: 102,419,528 (GRCm39)	I512V	probably benign	Het
Lamc1	A	T	1: 153,119,021 (GRCm39)	F866Y	possibly damaging	Het
Lbx1	C	A	19: 45,223,687 (GRCm39)		probably benign	Het
Magel2	A	G	7: 62,028,658 (GRCm39)	T521A	possibly damaging	Het
Mgam	A	T	6: 40,723,367 (GRCm39)	I491L	probably benign	Het
Mitd1	T	C	1: 37,929,273 (GRCm39)	E40G	probably damaging	Het
Mpzl3	A	G	9: 44,981,985 (GRCm39)	T218A	probably benign	Het
Mrpl42	A	G	10: 95,316,827 (GRCm39)	S77P	probably benign	Het
Mup5	C	T	4: 61,752,911 (GRCm39)	W37*	probably null	Het
Myh14	T	C	7: 44,281,850 (GRCm39)	I803V	probably benign	Het
Ncor2	T	A	5: 125,107,153 (GRCm39)	T744S		Het
Ndufv3	A	G	17: 31,746,596 (GRCm39)	D162G	probably damaging	Het
Nostrin	A	G	2: 69,006,150 (GRCm39)	E278G	probably damaging	Het
Nrxn1	T	G	17: 90,469,807 (GRCm39)	E1288A	probably benign	Het
Or4c11c	A	G	2: 88,661,472 (GRCm39)	N4D	possibly damaging	Het
Or51b6b	C	A	7: 103,310,088 (GRCm39)	R123L	probably damaging	Het
Or52h1	T	A	7: 103,828,955 (GRCm39)	Y220F	probably damaging	Het
Or8g55	A	T	9: 39,784,751 (GRCm39)	Y60F	possibly damaging	Het
Patj	T	A	4: 98,312,737 (GRCm39)		probably null	Het
Pcm1	T	G	8: 41,720,381 (GRCm39)	I314R	possibly damaging	Het
Pcsk6	A	G	7: 65,683,646 (GRCm39)	T754A	probably benign	Het
Pde2a	A	T	7: 101,152,041 (GRCm39)	N326I	probably benign	Het
Plekhg4	T	C	8: 106,105,316 (GRCm39)	S594P	possibly damaging	Het
Plekhm3	T	C	1: 64,977,065 (GRCm39)	D135G	probably damaging	Het
Plin4	A	T	17: 56,413,776 (GRCm39)	M283K	probably benign	Het
Ppfia3	T	C	7: 44,990,172 (GRCm39)		probably null	Het
Prrt3	T	C	6: 113,471,449 (GRCm39)	S908G	probably damaging	Het
Psg22	C	A	7: 18,456,660 (GRCm39)	S181Y	possibly damaging	Het
Rcor3	C	A	1: 191,822,173 (GRCm39)	G8V	probably damaging	Het
Rp1l1	T	A	14: 64,269,023 (GRCm39)	C1536*	probably null	Het
Rpp25l	T	C	4: 41,712,529 (GRCm39)	H82R	probably damaging	Het
Rps3a1	T	A	3: 86,046,396 (GRCm39)	M172L	probably benign	Het
Rtbdn	T	C	8: 85,679,556 (GRCm39)	L110P	probably damaging	Het
Ryr1	T	A	7: 28,778,010 (GRCm39)	Q2169L	probably damaging	Het
Scn4a	A	T	11: 106,211,299 (GRCm39)	C1573S	possibly damaging	Het
Sec16b	A	T	1: 157,358,965 (GRCm39)		probably null	Het
Serpina1a	A	T	12: 103,820,096 (GRCm39)	D383E	possibly damaging	Het
Sh3gl3	T	C	7: 81,934,285 (GRCm39)	M262T	probably benign	Het
Sos2	G	A	12: 69,637,654 (GRCm39)	T1052M	probably damaging	Het
Spag16	G	A	1: 70,036,000 (GRCm39)	V343I	probably benign	Het
Spocd1	T	G	4: 129,823,957 (GRCm39)	D251E		Het
Stc2	G	T	11: 31,317,798 (GRCm39)	N74K	probably damaging	Het
Tasor2	A	G	13: 3,623,621 (GRCm39)	Y2110H	probably damaging	Het
Thbs3	C	T	3: 89,126,359 (GRCm39)	Q227*	probably null	Het
Tmem92	A	C	11: 94,669,816 (GRCm39)	I105R	probably benign	Het
Tmod1	T	A	4: 46,083,632 (GRCm39)	N20K	probably benign	Het
Tns1	T	C	1: 73,992,638 (GRCm39)	D53G	probably damaging	Het
Tspan33	T	A	6: 29,717,337 (GRCm39)	L246Q	probably damaging	Het
Ttc16	A	G	2: 32,658,980 (GRCm39)	L392P	probably damaging	Het
Uggt1	T	A	1: 36,224,919 (GRCm39)	T572S	probably benign	Het
Usp17la	A	T	7: 104,509,604 (GRCm39)	T70S	probably damaging	Het
Usp31	C	T	7: 121,274,186 (GRCm39)	R370H	probably damaging	Het
Wdr83	C	T	8: 85,806,463 (GRCm39)	V112M	probably damaging	Het
Zbtb25	T	A	12: 76,416,366 (GRCm39)		probably benign	Het
Zfp110	T	A	7: 12,583,267 (GRCm39)	N638K	possibly damaging	Het
Zfp747l1	T	A	7: 126,984,455 (GRCm39)	S216C	probably benign	Het
Zfp820	T	C	17: 22,037,994 (GRCm39)	T445A	probably benign	Het

Other mutations in Prdm9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01302:Prdm9	APN	17	15,773,608 (GRCm39)	missense	probably benign	0.11
IGL02322:Prdm9	APN	17	15,783,110 (GRCm39)	missense	probably damaging	0.99
IGL02354:Prdm9	APN	17	15,783,109 (GRCm39)	missense	probably damaging	1.00
IGL02361:Prdm9	APN	17	15,783,109 (GRCm39)	missense	probably damaging	1.00
IGL02724:Prdm9	APN	17	15,783,522 (GRCm39)	missense	probably benign	0.07
IGL03120:Prdm9	APN	17	15,765,193 (GRCm39)	missense	probably benign
berlin	UTSW	17	15,782,702 (GRCm39)	missense	probably damaging	0.96
R0173:Prdm9	UTSW	17	15,764,297 (GRCm39)	missense	probably benign	0.00
R0173:Prdm9	UTSW	17	15,764,275 (GRCm39)	missense	probably benign	0.02
R0309:Prdm9	UTSW	17	15,777,646 (GRCm39)	missense	probably damaging	0.98
R1420:Prdm9	UTSW	17	15,764,638 (GRCm39)	missense	probably damaging	1.00
R3498:Prdm9	UTSW	17	15,783,207 (GRCm39)	splice site	probably benign
R3714:Prdm9	UTSW	17	15,777,623 (GRCm39)	nonsense	probably null
R4118:Prdm9	UTSW	17	15,764,275 (GRCm39)	missense	probably benign	0.02
R4369:Prdm9	UTSW	17	15,764,708 (GRCm39)	missense	probably benign	0.14
R4691:Prdm9	UTSW	17	15,773,640 (GRCm39)	missense	probably benign	0.03
R4742:Prdm9	UTSW	17	15,773,783 (GRCm39)	missense	probably damaging	0.99
R4910:Prdm9	UTSW	17	15,764,585 (GRCm39)	missense	probably benign	0.08
R5056:Prdm9	UTSW	17	15,782,679 (GRCm39)	missense	possibly damaging	0.93
R5130:Prdm9	UTSW	17	15,764,729 (GRCm39)	missense	probably benign	0.00
R5175:Prdm9	UTSW	17	15,777,713 (GRCm39)	missense	probably benign	0.04
R5187:Prdm9	UTSW	17	15,783,155 (GRCm39)	missense	probably damaging	0.98
R5213:Prdm9	UTSW	17	15,775,416 (GRCm39)	missense	probably damaging	0.98
R5270:Prdm9	UTSW	17	15,773,625 (GRCm39)	missense	probably benign	0.16
R5635:Prdm9	UTSW	17	15,782,702 (GRCm39)	missense	probably damaging	0.96
R6753:Prdm9	UTSW	17	15,765,218 (GRCm39)	missense	probably benign	0.00
R6857:Prdm9	UTSW	17	15,764,518 (GRCm39)	missense	probably benign	0.04
R7041:Prdm9	UTSW	17	15,765,257 (GRCm39)	missense	possibly damaging	0.56
R7355:Prdm9	UTSW	17	15,765,497 (GRCm39)	missense	probably benign	0.01
R7410:Prdm9	UTSW	17	15,765,259 (GRCm39)	missense	possibly damaging	0.73
R7571:Prdm9	UTSW	17	15,783,526 (GRCm39)	missense	probably damaging	0.98
R7575:Prdm9	UTSW	17	15,764,890 (GRCm39)	missense	probably damaging	1.00
R7593:Prdm9	UTSW	17	15,764,867 (GRCm39)	missense	possibly damaging	0.81
R7664:Prdm9	UTSW	17	15,775,833 (GRCm39)	missense	probably damaging	0.99
R7755:Prdm9	UTSW	17	15,765,226 (GRCm39)	missense	probably damaging	1.00
R7817:Prdm9	UTSW	17	15,779,311 (GRCm39)	missense	probably damaging	1.00
R7875:Prdm9	UTSW	17	15,773,804 (GRCm39)	nonsense	probably null
R8110:Prdm9	UTSW	17	15,774,960 (GRCm39)	missense	probably damaging	1.00
R8222:Prdm9	UTSW	17	15,765,035 (GRCm39)	missense	possibly damaging	0.93
R8405:Prdm9	UTSW	17	15,764,456 (GRCm39)	missense	probably benign	0.22
R8695:Prdm9	UTSW	17	15,765,019 (GRCm39)	missense	probably damaging	1.00
R8947:Prdm9	UTSW	17	15,764,270 (GRCm39)	missense	possibly damaging	0.96
X0021:Prdm9	UTSW	17	15,773,734 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GACATGATCTAGGTTCCACATGAC -3'
(R):5'- CAGTTGAATATGGGATCTTAGCTTC -3'

Sequencing Primer
(F):5'- GATCTAGGTTCCACATGACCAAATG -3'
(R):5'- CTGGAACTCACTTTGTAGACCAGG -3'

Posted On

2019-10-17