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

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

MMRRC Submission

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.317) question?

Stock #

R7570 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

15543079-15564354 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 15555652 bp (GRCm38)

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: 91,934,610	T613I	probably benign	Het
9130019O22Rik	T	A	7: 127,385,283	S216C	probably benign	Het
Ajuba	T	C	14: 54,576,402	E288G	probably damaging	Het
Ankrd12	C	T	17: 65,985,360	R1026K	probably benign	Het
Apol7b	T	C	15: 77,423,474	T274A	probably benign	Het
Arid4a	A	T	12: 71,063,142	R86*	probably null	Het
Asnsd1	C	T	1: 53,348,258	G70D	probably damaging	Het
Atg4c	T	A	4: 99,228,560	V313D	possibly damaging	Het
Atp13a5	A	C	16: 29,266,963	C885G	probably damaging	Het
Bpifb9a	A	T	2: 154,262,263	I209F	possibly damaging	Het
Bsn	T	C	9: 108,113,543	D1670G	probably damaging	Het
Cct8	T	A	16: 87,491,322	I121F	probably benign	Het
Cd209a	T	G	8: 3,744,151	D217A	probably damaging	Het
Cdk19	C	T	10: 40,477,958	S456L	possibly damaging	Het
Chd9	C	T	8: 90,994,580	H999Y	unknown	Het
Col5a1	G	A	2: 27,951,383	V339M	unknown	Het
Cr2	G	A	1: 195,169,340	R115*	probably null	Het
Cyb561	A	T	11: 105,937,644	F62I	probably damaging	Het
Cyp2c38	A	T	19: 39,404,743	N293K	possibly damaging	Het
Cyp2c69	A	T	19: 39,859,898	D293E	probably damaging	Het
Dcbld2	T	A	16: 58,424,569	C69S	possibly damaging	Het
Dcdc2a	T	C	13: 25,119,373	S296P	probably benign	Het
Dmxl1	T	A	18: 49,893,957	I2044K	possibly damaging	Het
Dnah5	A	G	15: 28,346,952	D2527G	probably damaging	Het
Dnah6	T	C	6: 73,149,430	T1305A	probably benign	Het
Dnajc9	A	G	14: 20,388,644	V47A	probably benign	Het
Dnmt3b	A	G	2: 153,676,699	Y594C	probably damaging	Het
Dph7	A	G	2: 24,965,630	D147G	probably damaging	Het
Drap1	T	C	19: 5,423,352	H164R	possibly damaging	Het
Dsg3	T	A	18: 20,527,780	V392E	possibly damaging	Het
Dxo	A	G	17: 34,837,640	D81G	probably benign	Het
E230025N22Rik	G	T	18: 36,695,592	T11K	probably benign	Het
Esyt1	A	G	10: 128,518,932	V533A	possibly damaging	Het
Etv3	T	A	3: 87,536,031	C307*	probably null	Het
Fam114a1	T	A	5: 65,030,059		probably null	Het
Fam208b	A	G	13: 3,573,621	Y2110H	probably damaging	Het
Fam3c	T	A	6: 22,326,405		probably benign	Het
Fbn1	G	T	2: 125,397,852	T305K	probably benign	Het
Ggt1	A	T	10: 75,585,594	I484F	probably damaging	Het
Gm10639	A	T	9: 78,304,469	D171V	possibly damaging	Het
Gpatch1	T	C	7: 35,293,812	D536G	probably damaging	Het
Gpx4	T	C	10: 80,055,041	I189T	probably damaging	Het
Gsr	T	A	8: 33,669,165	C85S	probably damaging	Het
Havcr1	T	A	11: 46,770,542		probably null	Het
Heatr4	T	C	12: 83,979,644	T280A	probably benign	Het
Hmcn2	A	T	2: 31,423,911	E3532D	probably benign	Het
Hnrnpc	T	C	14: 52,075,099	N308S	possibly damaging	Het
Ighv8-9	A	G	12: 115,468,738	V13A	probably benign	Het
Itgb2l	A	T	16: 96,426,239	F535I	probably benign	Het
Kdm5a	T	G	6: 120,427,842	D1348E	probably damaging	Het
Kndc1	CT	C	7: 139,923,775		probably null	Het
Ky	A	G	9: 102,542,329	I512V	probably benign	Het
Lamc1	A	T	1: 153,243,275	F866Y	possibly damaging	Het
Lbx1	C	A	19: 45,235,248		probably benign	Het
Magel2	A	G	7: 62,378,910	T521A	possibly damaging	Het
Mgam	A	T	6: 40,746,433	I491L	probably benign	Het
Mitd1	T	C	1: 37,890,192	E40G	probably damaging	Het
Mpzl3	A	G	9: 45,070,687	T218A	probably benign	Het
Mrpl42	A	G	10: 95,480,965	S77P	probably benign	Het
Mup5	C	T	4: 61,834,674	W37*	probably null	Het
Myh14	T	C	7: 44,632,426	I803V	probably benign	Het
Ncor2	T	A	5: 125,030,089	T744S		Het
Ndufv3	A	G	17: 31,527,622	D162G	probably damaging	Het
Nostrin	A	G	2: 69,175,806	E278G	probably damaging	Het
Nrxn1	T	G	17: 90,162,379	E1288A	probably benign	Het
Olfr1205	A	G	2: 88,831,128	N4D	possibly damaging	Het
Olfr623	C	A	7: 103,660,881	R123L	probably damaging	Het
Olfr648	T	A	7: 104,179,748	Y220F	probably damaging	Het
Olfr972	A	T	9: 39,873,455	Y60F	possibly damaging	Het
Patj	T	A	4: 98,424,500		probably null	Het
Pcm1	T	G	8: 41,267,344	I314R	possibly damaging	Het
Pcsk6	A	G	7: 66,033,898	T754A	probably benign	Het
Pde2a	A	T	7: 101,502,834	N326I	probably benign	Het
Plekhg4	T	C	8: 105,378,684	S594P	possibly damaging	Het
Plekhm3	T	C	1: 64,937,906	D135G	probably damaging	Het
Plin4	A	T	17: 56,106,776	M283K	probably benign	Het
Ppfia3	T	C	7: 45,340,748		probably null	Het
Prrt3	T	C	6: 113,494,488	S908G	probably damaging	Het
Psg22	C	A	7: 18,722,735	S181Y	possibly damaging	Het
Rcor3	C	A	1: 192,137,876	G8V	probably damaging	Het
Rp1l1	T	A	14: 64,031,574	C1536*	probably null	Het
Rpp25l	T	C	4: 41,712,529	H82R	probably damaging	Het
Rps3a1	T	A	3: 86,139,089	M172L	probably benign	Het
Rtbdn	T	C	8: 84,952,927	L110P	probably damaging	Het
Ryr1	T	A	7: 29,078,585	Q2169L	probably damaging	Het
Scn4a	A	T	11: 106,320,473	C1573S	possibly damaging	Het
Sec16b	A	T	1: 157,531,395		probably null	Het
Serpina1a	A	T	12: 103,853,837	D383E	possibly damaging	Het
Sh3gl3	T	C	7: 82,285,077	M262T	probably benign	Het
Sos2	G	A	12: 69,590,880	T1052M	probably damaging	Het
Spag16	G	A	1: 69,996,841	V343I	probably benign	Het
Spocd1	T	G	4: 129,930,164	D251E		Het
Stc2	G	T	11: 31,367,798	N74K	probably damaging	Het
Thbs3	C	T	3: 89,219,052	Q227*	probably null	Het
Tmem92	A	C	11: 94,778,990	I105R	probably benign	Het
Tmod1	T	A	4: 46,083,632	N20K	probably benign	Het
Tns1	T	C	1: 73,953,479	D53G	probably damaging	Het
Tspan33	T	A	6: 29,717,338	L246Q	probably damaging	Het
Ttc16	A	G	2: 32,768,968	L392P	probably damaging	Het
Uggt1	T	A	1: 36,185,838	T572S	probably benign	Het
Usp17la	A	T	7: 104,860,397	T70S	probably damaging	Het
Usp31	C	T	7: 121,674,963	R370H	probably damaging	Het
Wdr83	C	T	8: 85,079,834	V112M	probably damaging	Het
Zbtb25	T	A	12: 76,369,592		probably benign	Het
Zfp110	T	A	7: 12,849,340	N638K	possibly damaging	Het
Zfp820	T	C	17: 21,819,013	T445A	probably benign	Het

Other mutations in Prdm9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01302:Prdm9	APN	17	15553346	missense	probably benign	0.11
IGL02322:Prdm9	APN	17	15562848	missense	probably damaging	0.99
IGL02354:Prdm9	APN	17	15562847	missense	probably damaging	1.00
IGL02361:Prdm9	APN	17	15562847	missense	probably damaging	1.00
IGL02724:Prdm9	APN	17	15563260	missense	probably benign	0.07
IGL03120:Prdm9	APN	17	15544931	missense	probably benign
berlin	UTSW	17	15562440	missense	probably damaging	0.96
R0173:Prdm9	UTSW	17	15544013	missense	probably benign	0.02
R0173:Prdm9	UTSW	17	15544035	missense	probably benign	0.00
R0309:Prdm9	UTSW	17	15557384	missense	probably damaging	0.98
R1420:Prdm9	UTSW	17	15544376	missense	probably damaging	1.00
R3498:Prdm9	UTSW	17	15562945	splice site	probably benign
R3714:Prdm9	UTSW	17	15557361	nonsense	probably null
R4118:Prdm9	UTSW	17	15544013	missense	probably benign	0.02
R4369:Prdm9	UTSW	17	15544446	missense	probably benign	0.14
R4691:Prdm9	UTSW	17	15553378	missense	probably benign	0.03
R4742:Prdm9	UTSW	17	15553521	missense	probably damaging	0.99
R4910:Prdm9	UTSW	17	15544323	missense	probably benign	0.08
R5056:Prdm9	UTSW	17	15562417	missense	possibly damaging	0.93
R5130:Prdm9	UTSW	17	15544467	missense	probably benign	0.00
R5175:Prdm9	UTSW	17	15557451	missense	probably benign	0.04
R5187:Prdm9	UTSW	17	15562893	missense	probably damaging	0.98
R5213:Prdm9	UTSW	17	15555154	missense	probably damaging	0.98
R5270:Prdm9	UTSW	17	15553363	missense	probably benign	0.16
R5635:Prdm9	UTSW	17	15562440	missense	probably damaging	0.96
R6753:Prdm9	UTSW	17	15544956	missense	probably benign	0.00
R6857:Prdm9	UTSW	17	15544256	missense	probably benign	0.04
R7041:Prdm9	UTSW	17	15544995	missense	possibly damaging	0.56
R7355:Prdm9	UTSW	17	15545235	missense	probably benign	0.01
R7410:Prdm9	UTSW	17	15544997	missense	possibly damaging	0.73
R7571:Prdm9	UTSW	17	15563264	missense	probably damaging	0.98
R7575:Prdm9	UTSW	17	15544628	missense	probably damaging	1.00
R7593:Prdm9	UTSW	17	15544605	missense	possibly damaging	0.81
R7664:Prdm9	UTSW	17	15555571	missense	probably damaging	0.99
R7755:Prdm9	UTSW	17	15544964	missense	probably damaging	1.00
R7817:Prdm9	UTSW	17	15559049	missense	probably damaging	1.00
R7875:Prdm9	UTSW	17	15553542	nonsense	probably null
R8110:Prdm9	UTSW	17	15554698	missense	probably damaging	1.00
R8222:Prdm9	UTSW	17	15544773	missense	possibly damaging	0.93
R8405:Prdm9	UTSW	17	15544194	missense	probably benign	0.22
R8695:Prdm9	UTSW	17	15544757	missense	probably damaging	1.00
R8947:Prdm9	UTSW	17	15544008	missense	possibly damaging	0.96
X0021:Prdm9	UTSW	17	15553472	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