Mutagenetix > Incidental Mutations

Incidental Mutation 'R5056:Prdm9'

450632

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

042646-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.389) question?

Stock #

R5056 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

15543079-15564354 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 15562417 bp

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Arginine at position 104 (Q104R)

Ref Sequence

ENSEMBL: ENSMUSP00000131871 (fasta)

Gene Model

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132675

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139911

Predicted Effect

probably benign
Transcript: ENSMUST00000147532

SMART Domains

Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000167994
AA Change: Q104R

PolyPhen 2 Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: Q104R

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000178455

SMART Domains

Protein: ENSMUSP00000137164
Gene: ENSMUSG00000095920

Domain	Start	End	E-Value	Type
Pfam:Ribosomal_S21	11	50	1.4e-13	PFAM

Meta Mutation Damage Score

0.0934

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.0%
20x: 91.2%

Validation Efficiency

99% (73/74)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030J22Rik	T	A	8: 116,971,682	K229*	probably null	Het
9930021J03Rik	A	T	19: 29,717,359	I1578K	probably benign	Het
Adora2a	T	A	10: 75,326,158	S44T	probably damaging	Het
Agap3	T	C	5: 24,477,862	V459A	probably damaging	Het
Apc2	T	C	10: 80,301,314	V31A	probably benign	Het
Asic2	T	A	11: 80,971,603	K189N	possibly damaging	Het
Bbs10	C	T	10: 111,300,540	P505S	probably benign	Het
C87414	T	C	5: 93,638,925		probably benign	Het
Cdh20	G	T	1: 104,953,997	V396L	probably benign	Het
Cenpb	C	T	2: 131,178,171		probably benign	Het
Chil6	T	A	3: 106,394,343	Y147F	probably damaging	Het
Cluh	C	T	11: 74,661,946	R606C	probably damaging	Het
Cmtr1	A	G	17: 29,690,328	T404A	possibly damaging	Het
Cnot1	T	C	8: 95,741,008	N1499S	probably damaging	Het
Dmkn	T	C	7: 30,764,104	S61P	probably damaging	Het
Dmxl1	T	C	18: 49,870,923	C872R	probably benign	Het
Dnah3	A	G	7: 120,020,946	Y1587H	probably damaging	Het
Dsc2	A	T	18: 20,050,142	V73D	probably damaging	Het
F5	A	T	1: 164,192,032	Y692F	possibly damaging	Het
Fam184a	A	T	10: 53,674,574	L80I	probably damaging	Het
Fam46b	C	T	4: 133,480,438	R47W	possibly damaging	Het
Foxj2	A	G	6: 122,833,874	H271R	probably benign	Het
Grm7	A	G	6: 111,080,443	T335A	probably damaging	Het
Hspa9	A	G	18: 34,938,681	L622P	probably damaging	Het
Kcna7	G	A	7: 45,406,591	R77H	probably damaging	Het
Kcnd3	T	A	3: 105,666,928		probably benign	Het
Klhdc8b	ACACGCACGCACGCACGCACGCACGCACGCACGCACGCAC	ACACGCACGCACGCACGCACGCACGCACGCACGCACGCACGCAC	9: 108,448,985		probably benign	Het
Klk14	G	A	7: 43,692,077	C51Y	probably damaging	Het
Lrch4	C	G	5: 137,636,851	N237K	probably damaging	Het
Lss	T	G	10: 76,552,926		probably null	Het
Map6	T	C	7: 99,336,652	F588L	probably benign	Het
Mbd6	C	T	10: 127,286,441	V173I	probably benign	Het
Med13	A	T	11: 86,328,565	S352T	probably benign	Het
Mettl16	T	A	11: 74,816,940	V320E	probably benign	Het
Myh7b	G	C	2: 155,632,373	R1669S	possibly damaging	Het
Nup188	T	A	2: 30,304,131	D149E	probably damaging	Het
Ogfrl1	A	G	1: 23,379,049	S83P	probably damaging	Het
Olfr1025-ps1	T	A	2: 85,918,136	D70E	probably damaging	Het
Olfr1083-ps	T	A	2: 86,607,020	I184F	unknown	Het
Olfr1154	T	C	2: 87,903,571	Y35C	probably damaging	Het
Olfr685	T	A	7: 105,180,572	H262L	probably damaging	Het
Pafah1b3	C	T	7: 25,295,339	R98Q	probably damaging	Het
Pde6b	A	T	5: 108,423,491	K437*	probably null	Het
Ppp1r12b	A	T	1: 134,834,392		probably benign	Het
Ppp1r12b	G	T	1: 134,955,733	A17E	probably benign	Het
Rgs22	A	T	15: 36,050,245		probably null	Het
Rnf14	C	T	18: 38,308,388	P277L	probably damaging	Het
Robo4	T	C	9: 37,404,806	S258P	probably benign	Het
Sfrp1	T	A	8: 23,417,404	F207I	probably damaging	Het
Sgms1	A	G	19: 32,159,687	S160P	probably damaging	Het
Sil1	T	C	18: 35,269,702	K263R	probably benign	Het
St14	A	G	9: 31,097,551		probably null	Het
Syne2	A	G	12: 75,909,131		probably benign	Het
Tbc1d9	T	C	8: 83,269,206	S1013P	probably benign	Het
Tmem67	T	C	4: 12,070,471	S352G	probably benign	Het
Trib2	C	A	12: 15,793,794	K282N	possibly damaging	Het
Trnau1ap	T	C	4: 132,327,171		probably benign	Het
Trpm4	T	C	7: 45,308,630	D952G	probably damaging	Het
Unc93b1	A	G	19: 3,942,762	N305D	possibly damaging	Het
Usp32	A	G	11: 85,026,795	V802A	probably benign	Het
Vmn2r48	T	A	7: 9,942,324	H410L	probably damaging	Het
Wfs1	T	C	5: 36,975,587	N116S	probably benign	Het
Wif1	A	T	10: 121,099,779	H333L	probably benign	Het
Zfp109	T	C	7: 24,228,737	T416A	possibly damaging	Het
Zfp808	T	A	13: 62,172,630	C558S	probably damaging	Het
Zpbp	T	C	11: 11,459,734	D116G	possibly damaging	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
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
R7570:Prdm9	UTSW	17	15555652	missense	probably benign	0.14
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
R7958:Prdm9	UTSW	17	15553542	nonsense	probably null
X0021:Prdm9	UTSW	17	15553472	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TGCTTATCCTAGCTACTTTGGG -3'
(R):5'- CCTGGCCTTGTGATACATTTG -3'

Sequencing Primer
(F):5'- TGATATTTCTTGTTCATGCCCAG -3'
(R):5'- GATACATTTGTTCCATCCTCTAGGG -3'

Posted On

2016-12-27