Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02361:Prdm9'

290495

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Prdm9

Ensembl Gene

ENSMUSG00000051977

Gene Name

PR domain containing 9

Synonyms

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

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.435) question?

Stock #

IGL02361

Quality Score

Status

Chromosome

Chromosomal Location

15543079-15564354 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 15562847 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 58 (V58M)

Ref Sequence

ENSEMBL: ENSMUSP00000131871 (fasta)

Gene Model

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

AlphaFold

Q96EQ9

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

probably damaging
Transcript: ENSMUST00000167994
AA Change: V58M

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: V58M

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

Coding Region Coverage

Validation Efficiency

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aqp1	A	C	6: 55,345,513	L164F	possibly damaging	Het
Bfsp1	T	C	2: 143,831,987	E261G	probably damaging	Het
Brinp2	A	G	1: 158,247,178	C458R	probably damaging	Het
Cacng3	T	G	7: 122,671,946	M58R	possibly damaging	Het
Cfap43	A	T	19: 47,897,413	C254*	probably null	Het
Cnga1	T	C	5: 72,616,718		probably null	Het
Dis3	A	T	14: 99,079,712	Y765*	probably null	Het
Dpep1	T	A	8: 123,200,218	S260R	probably benign	Het
Elmod1	A	G	9: 53,931,558	L106P	probably damaging	Het
Fut10	A	G	8: 31,201,370	Y81C	probably damaging	Het
Fzd10	T	A	5: 128,601,868	D217E	possibly damaging	Het
Gap43	T	C	16: 42,340,508		probably benign	Het
Gigyf1	T	C	5: 137,519,727		probably benign	Het
Gm1840	T	C	8: 5,640,896		noncoding transcript	Het
Gpc5	C	T	14: 115,133,287	R175*	probably null	Het
Kcna1	C	A	6: 126,642,906	Q150H	probably damaging	Het
Lama5	A	T	2: 180,193,884	C1225*	probably null	Het
Lrrc25	A	T	8: 70,617,827	D86V	probably benign	Het
Madd	A	T	2: 91,162,198	V1043E	probably benign	Het
Mov10	A	T	3: 104,804,121		probably benign	Het
Mzb1	T	A	18: 35,649,197	H46L	possibly damaging	Het
Nek10	A	T	14: 14,843,856	Q193L	probably damaging	Het
Nos3	A	T	5: 24,367,623	I187F	probably damaging	Het
Olfr1231	T	A	2: 89,303,182	M137L	probably benign	Het
Olfr473	T	A	7: 107,934,277	Y252*	probably null	Het
Olfr822	A	G	10: 130,075,274	Y288C	probably damaging	Het
Pgap1	T	C	1: 54,512,816	T486A	probably benign	Het
Prkd2	A	G	7: 16,847,658	Y146C	probably damaging	Het
Psmd9	G	T	5: 123,248,316	R175I	probably damaging	Het
Pxdn	A	G	12: 29,999,189	D618G	probably damaging	Het
Rgs6	A	T	12: 82,618,619		probably benign	Het
Rrm2	G	T	12: 24,711,439		probably benign	Het
Shank3	T	C	15: 89,504,333	V376A	probably damaging	Het
Slc5a10	A	G	11: 61,719,840		probably null	Het
Slfn3	A	T	11: 83,213,242	Q313L	possibly damaging	Het
Sptbn1	A	T	11: 30,110,783	F2062L	probably damaging	Het
Tbc1d10a	T	C	11: 4,215,047	V500A	probably benign	Het
Tcea1	T	C	1: 4,896,347		probably benign	Het
Thsd7a	T	C	6: 12,348,193		probably benign	Het
Tm9sf4	C	T	2: 153,187,650	T173M	probably benign	Het
Tmtc2	T	C	10: 105,271,526	T709A	probably benign	Het
Zfp385b	T	C	2: 77,450,303	E97G	probably damaging	Het
Zim1	A	T	7: 6,682,874		probably null	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
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
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
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

Posted On

2015-04-16