Incidental Mutation 'R4691:Prdm9'
| ID |
354943 |
| 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 |
041942-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.297)
|
| Stock # |
R4691 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 15773640 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Threonine
at position 252
(M252T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000118454
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000147532]
[ENSMUST00000167994]
|
| AlphaFold |
Q96EQ9 |
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128267
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130297
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000147532
AA Change: M252T
PolyPhen 2
Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977
AA Change: M252T
| 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: M377T
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: M377T
| 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: ENSMUST00000231919
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.0%
|
| Validation Efficiency |
97% (70/72) |
| 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 |
|---|
| Abca13 |
A |
T |
11: 9,384,195 (GRCm39) |
R3882S |
probably damaging |
Het |
| Adamts2 |
G |
T |
11: 50,647,523 (GRCm39) |
V299F |
probably damaging |
Het |
| Ankrd50 |
A |
G |
3: 38,537,159 (GRCm39) |
S65P |
probably benign |
Het |
| Ap4e1 |
T |
C |
2: 126,903,791 (GRCm39) |
C898R |
probably benign |
Het |
| Arel1 |
A |
T |
12: 84,977,023 (GRCm39) |
|
probably null |
Het |
| Bag6 |
T |
A |
17: 35,358,224 (GRCm39) |
V164D |
probably damaging |
Het |
| C2cd5 |
A |
G |
6: 142,975,874 (GRCm39) |
S769P |
possibly damaging |
Het |
| Cables1 |
C |
T |
18: 11,973,580 (GRCm39) |
Q240* |
probably null |
Het |
| Ccnb1-ps |
T |
A |
7: 41,755,516 (GRCm39) |
|
noncoding transcript |
Het |
| Ccz1 |
A |
T |
5: 143,928,380 (GRCm39) |
I390N |
possibly damaging |
Het |
| Ceacam23 |
T |
A |
7: 17,642,891 (GRCm39) |
S434T |
possibly damaging |
Het |
| Ces1a |
T |
C |
8: 93,759,287 (GRCm39) |
H283R |
probably benign |
Het |
| Clca3b |
G |
A |
3: 144,544,853 (GRCm39) |
T378I |
probably benign |
Het |
| Cpne2 |
A |
T |
8: 95,284,849 (GRCm39) |
I342F |
probably damaging |
Het |
| Cyp2d9 |
A |
G |
15: 82,340,033 (GRCm39) |
D141G |
probably damaging |
Het |
| Ddias |
T |
A |
7: 92,508,024 (GRCm39) |
K630N |
probably damaging |
Het |
| Dennd4b |
A |
G |
3: 90,179,619 (GRCm39) |
T626A |
probably damaging |
Het |
| Disc1 |
T |
C |
8: 125,875,186 (GRCm39) |
V554A |
possibly damaging |
Het |
| Dnah10 |
A |
G |
5: 124,852,581 (GRCm39) |
T1880A |
probably damaging |
Het |
| Dnase1l1 |
C |
T |
X: 73,320,644 (GRCm39) |
|
probably null |
Het |
| Epop |
C |
T |
11: 97,519,719 (GRCm39) |
G130D |
possibly damaging |
Het |
| Erap1 |
T |
C |
13: 74,821,811 (GRCm39) |
L722P |
probably damaging |
Het |
| Eya4 |
T |
A |
10: 23,015,966 (GRCm39) |
T334S |
probably benign |
Het |
| Ezr |
T |
C |
17: 7,026,961 (GRCm39) |
I5V |
probably benign |
Het |
| Fam53c |
A |
C |
18: 34,901,743 (GRCm39) |
E220A |
probably damaging |
Het |
| Galnt12 |
T |
C |
4: 47,104,143 (GRCm39) |
S134P |
probably damaging |
Het |
| Gcfc2 |
T |
A |
6: 81,918,408 (GRCm39) |
L366* |
probably null |
Het |
| Gins4 |
T |
A |
8: 23,727,075 (GRCm39) |
D6V |
probably benign |
Het |
| Grid1 |
A |
G |
14: 35,291,514 (GRCm39) |
H807R |
probably benign |
Het |
| H2-T22 |
GTTTT |
GTTT |
17: 36,352,462 (GRCm39) |
|
probably null |
Het |
| Ighv1-66 |
T |
C |
12: 115,556,929 (GRCm39) |
Y51C |
probably benign |
Het |
| Inpp4b |
A |
T |
8: 82,849,282 (GRCm39) |
Y901F |
probably damaging |
Het |
| Irf2 |
T |
A |
8: 47,299,222 (GRCm39) |
S339T |
probably damaging |
Het |
| Itgae |
G |
T |
11: 73,010,345 (GRCm39) |
G612* |
probably null |
Het |
| Kdr |
T |
C |
5: 76,105,259 (GRCm39) |
K1037R |
possibly damaging |
Het |
| Mro |
A |
T |
18: 74,006,397 (GRCm39) |
M115L |
probably benign |
Het |
| Myo5a |
A |
G |
9: 75,087,438 (GRCm39) |
E1098G |
probably damaging |
Het |
| Nkx2-1 |
T |
A |
12: 56,580,350 (GRCm39) |
M197L |
probably benign |
Het |
| Or7e165 |
T |
C |
9: 19,694,678 (GRCm39) |
I83T |
probably benign |
Het |
| Pank2 |
T |
A |
2: 131,138,201 (GRCm39) |
F430L |
possibly damaging |
Het |
| Pcx |
T |
A |
19: 4,669,505 (GRCm39) |
V794E |
probably damaging |
Het |
| Pdgfd |
C |
T |
9: 6,288,556 (GRCm39) |
P70L |
probably damaging |
Het |
| Pla2g4e |
T |
C |
2: 120,004,781 (GRCm39) |
Y521C |
probably damaging |
Het |
| Pou5f1 |
T |
A |
17: 35,817,028 (GRCm39) |
F11Y |
probably damaging |
Het |
| Ptk2b |
C |
T |
14: 66,394,518 (GRCm39) |
G859S |
probably benign |
Het |
| Rad51ap1 |
A |
G |
6: 126,904,516 (GRCm39) |
S123P |
probably benign |
Het |
| Robo3 |
T |
C |
9: 37,336,514 (GRCm39) |
E418G |
probably damaging |
Het |
| Sos2 |
C |
T |
12: 69,663,102 (GRCm39) |
R631H |
probably damaging |
Het |
| Sp140l1 |
C |
T |
1: 85,066,521 (GRCm39) |
|
probably benign |
Het |
| St3gal2 |
C |
T |
8: 111,684,417 (GRCm39) |
T25I |
probably benign |
Het |
| Stra6l |
G |
A |
4: 45,882,851 (GRCm39) |
A521T |
probably benign |
Het |
| Syt7 |
T |
A |
19: 10,403,845 (GRCm39) |
L177Q |
probably damaging |
Het |
| Tet2 |
T |
A |
3: 133,191,844 (GRCm39) |
Q863H |
possibly damaging |
Het |
| Tmem232 |
T |
C |
17: 65,572,237 (GRCm39) |
K585E |
possibly damaging |
Het |
| Trpc6 |
A |
C |
9: 8,652,979 (GRCm39) |
E595A |
probably damaging |
Het |
| Txnl1 |
A |
G |
18: 63,804,750 (GRCm39) |
V248A |
possibly damaging |
Het |
| Vmn2r72 |
A |
T |
7: 85,387,119 (GRCm39) |
L815* |
probably null |
Het |
| Vmn2r81 |
C |
T |
10: 79,129,211 (GRCm39) |
Q701* |
probably null |
Het |
| Vps13c |
T |
C |
9: 67,860,217 (GRCm39) |
V2811A |
possibly damaging |
Het |
| Vsig10l2 |
T |
C |
9: 35,428,158 (GRCm39) |
S106G |
possibly damaging |
Het |
| Zfp354a |
A |
G |
11: 50,961,064 (GRCm39) |
E425G |
probably damaging |
Het |
| Zfp617 |
A |
T |
8: 72,686,659 (GRCm39) |
T330S |
probably benign |
Het |
| Zfp663 |
G |
T |
2: 165,201,050 (GRCm39) |
|
probably benign |
Het |
| Zfp84 |
T |
C |
7: 29,476,505 (GRCm39) |
L399P |
probably damaging |
Het |
| Zfp869 |
A |
T |
8: 70,159,513 (GRCm39) |
C353* |
probably null |
Het |
| Zscan22 |
C |
T |
7: 12,640,488 (GRCm39) |
A85V |
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 |
|
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 |
|
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'- AGCTTTGGCACTTGACATTG -3'
(R):5'- GAGCTGCCTGCCTGATATTTTC -3'
Sequencing Primer
(F):5'- AGCTTTGGCACTTGACATTGTACTC -3'
(R):5'- TCCTTCCACTCTAGGTATGTGAACTG -3'
|
| Posted On |
2015-10-21 |
Incidental Mutation