Mutagenetix > Incidental Mutation

Incidental Mutation 'R7410:Prdm9'

575043

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

045491-MU

Accession Numbers

Essential gene?

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

Stock #

R7410 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

15763341-15784616 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 15765259 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 507 (I507T)

Ref Sequence

ENSEMBL: ENSMUSP00000131871 (fasta)

Gene Model

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

AlphaFold

Q96EQ9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000167994
AA Change: I507T

PolyPhen 2 Score 0.725 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: I507T

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210017I01Rik	A	G	3: 92,512,551 (GRCm39)	S3P	unknown	Het
Adgrv1	A	T	13: 81,711,738 (GRCm39)	D1079E	probably benign	Het
Agbl5	A	T	5: 31,048,032 (GRCm39)	Y102F	possibly damaging	Het
Ankfy1	T	C	11: 72,652,330 (GRCm39)	L1094S	probably damaging	Het
Ankrd42	A	T	7: 92,259,762 (GRCm39)	V337E	possibly damaging	Het
Axl	A	G	7: 25,458,208 (GRCm39)	L849P	probably benign	Het
Bmpr2	T	C	1: 59,907,652 (GRCm39)	I915T	probably benign	Het
Cables1	T	A	18: 12,074,282 (GRCm39)	F494L	probably benign	Het
Cacna1e	A	C	1: 154,347,980 (GRCm39)	V927G	probably benign	Het
Cavin1	A	T	11: 100,849,670 (GRCm39)	V320E	probably damaging	Het
Cemip	T	G	7: 83,602,042 (GRCm39)	S916R	probably damaging	Het
Cep57	G	A	9: 13,729,980 (GRCm39)		probably benign	Het
Ces1d	T	C	8: 93,919,433 (GRCm39)	N120D	probably damaging	Het
Cfap44	A	T	16: 44,288,776 (GRCm39)	S1509C	probably damaging	Het
Chga	A	G	12: 102,528,866 (GRCm39)	D281G	probably benign	Het
Clstn2	A	G	9: 97,423,920 (GRCm39)	F282L	probably benign	Het
Cnot1	A	T	8: 96,459,787 (GRCm39)	V1855E	possibly damaging	Het
Cnr1	T	A	4: 33,944,119 (GRCm39)	V169D	probably damaging	Het
Cpd	T	A	11: 76,673,134 (GRCm39)	H1337L	probably damaging	Het
Crabp2	T	A	3: 87,859,585 (GRCm39)	D78E	probably damaging	Het
Crat	C	T	2: 30,294,577 (GRCm39)	R497Q	probably benign	Het
Cyp2ab1	G	A	16: 20,135,475 (GRCm39)	A9V	probably benign	Het
Cyp3a41b	T	C	5: 145,514,967 (GRCm39)	D86G	probably damaging	Het
Dner	T	A	1: 84,563,332 (GRCm39)	D96V	probably damaging	Het
Duox1	C	A	2: 122,176,874 (GRCm39)	T1465N	probably damaging	Het
Ehd3	T	A	17: 74,112,428 (GRCm39)	V64E	probably benign	Het
Ehmt1	A	G	2: 24,738,080 (GRCm39)	V508A	probably benign	Het
Ephb3	G	A	16: 21,040,158 (GRCm39)	V761I	possibly damaging	Het
Fam161b	T	C	12: 84,404,575 (GRCm39)	Q35R	probably benign	Het
Fam186a	T	A	15: 99,844,826 (GRCm39)	K473*	probably null	Het
Fam227b	A	T	2: 125,960,983 (GRCm39)	D215E	probably damaging	Het
Fkbp15	C	A	4: 62,258,536 (GRCm39)	D144Y	probably damaging	Het
Galt	T	C	4: 41,757,707 (GRCm39)	I259T	possibly damaging	Het
Gbp11	G	A	5: 105,491,774 (GRCm39)	P8S	probably damaging	Het
Gfap	A	T	11: 102,783,963 (GRCm39)	M339K	probably damaging	Het
Gm14443	C	T	2: 175,011,069 (GRCm39)	R459Q	possibly damaging	Het
Grip1	A	G	10: 119,855,925 (GRCm39)	N632S	probably benign	Het
H4c18	G	A	13: 22,016,211 (GRCm39)	R40W	probably damaging	Het
Hcar1	T	G	5: 124,017,161 (GRCm39)	I177L	possibly damaging	Het
Ighv1-37	A	G	12: 114,860,099 (GRCm39)	V37A	probably damaging	Het
Ilf3	T	A	9: 21,311,100 (GRCm39)	F657L	unknown	Het
Ints2	T	G	11: 86,124,052 (GRCm39)	T579P	probably benign	Het
Iqgap1	G	T	7: 80,372,778 (GRCm39)	Y1520*	probably null	Het
Kdm4a	T	C	4: 118,001,115 (GRCm39)	H884R	possibly damaging	Het
Krtap19-1	A	T	16: 88,666,132 (GRCm39)	Y52N	unknown	Het
Lama5	A	T	2: 179,844,183 (GRCm39)		probably null	Het
Lrrc72	T	C	12: 36,272,803 (GRCm39)	N89D	probably damaging	Het
Med13l	A	G	5: 118,698,897 (GRCm39)	D16G	possibly damaging	Het
Mefv	A	G	16: 3,533,545 (GRCm39)	L242P	probably damaging	Het
Mob3c	T	C	4: 115,688,784 (GRCm39)	Y106H	probably damaging	Het
Nlrp1a	A	G	11: 71,014,683 (GRCm39)	I189T	probably damaging	Het
Nudt7	T	C	8: 114,860,559 (GRCm39)		probably benign	Het
Or13p10	T	C	4: 118,523,629 (GRCm39)	L305P	probably benign	Het
Or4f7	T	A	2: 111,644,271 (GRCm39)	I267L	probably benign	Het
Pappa	A	G	4: 65,253,956 (GRCm39)	T1537A	probably damaging	Het
Pik3r4	T	A	9: 105,527,790 (GRCm39)	V381E	probably damaging	Het
Pkd1	T	A	17: 24,794,855 (GRCm39)	Y2181N	probably damaging	Het
Pmel	G	T	10: 128,552,353 (GRCm39)	V396F	probably benign	Het
Psme4	C	T	11: 30,765,279 (GRCm39)	Q549*	probably null	Het
Ptprg	T	A	14: 11,962,657 (GRCm38)	W152R	probably damaging	Het
Ptprm	A	C	17: 67,000,561 (GRCm39)	V1141G	probably damaging	Het
Rapgef5	G	A	12: 117,685,063 (GRCm39)	V505M	probably damaging	Het
Rnf213	T	A	11: 119,325,877 (GRCm39)	M1558K		Het
Slc35a1	A	G	4: 34,675,034 (GRCm39)	V168A	probably benign	Het
Srebf1	T	C	11: 60,096,693 (GRCm39)	T347A	probably benign	Het
Stard9	T	A	2: 120,531,978 (GRCm39)	V2745D	probably benign	Het
Taar7e	A	T	10: 23,914,424 (GRCm39)	T305S	probably benign	Het
Tie1	T	C	4: 118,337,074 (GRCm39)	S551G	probably benign	Het
Tmc5	T	A	7: 118,222,820 (GRCm39)	Y173*	probably null	Het
Tns2	T	A	15: 102,018,961 (GRCm39)	V384D	probably damaging	Het
Tubgcp4	T	A	2: 121,014,890 (GRCm39)	Y267N	probably damaging	Het
Vmn1r53	A	G	6: 90,200,700 (GRCm39)	V208A	probably damaging	Het
Vwa8	A	C	14: 79,219,674 (GRCm39)		probably null	Het
Wdfy4	T	C	14: 32,696,191 (GRCm39)	D2784G		Het
Zfp712	A	C	13: 67,189,400 (GRCm39)	S376A	probably benign	Het
Znrf3	C	T	11: 5,238,955 (GRCm39)	C232Y	unknown	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
R7570:Prdm9	UTSW	17	15,775,914 (GRCm39)	missense	probably benign	0.14
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'- CCCTGCAAACATAGGGCTTC -3'
(R):5'- AGCTTCAGGAACAACATGTTGATTC -3'

Sequencing Primer
(F):5'- GGCTTCTCCCCTGTGTGTG -3'
(R):5'- GGAACAACATGTTGATTCACAGAAC -3'

Posted On

2019-10-07