Incidental Mutation 'R8110:Prdm9'
| ID |
630837 |
| 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 |
067539-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.301)
|
| Stock # |
R8110 (G1)
|
| Quality Score |
209.009 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
15543079-15564354 bp(-) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 15554698 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Tyrosine
at position 318
(N318Y)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000131871
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000147532]
[ENSMUST00000167994]
|
| AlphaFold |
Q96EQ9 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000147532
AA Change: N193Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977
AA Change: N193Y
| 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: N318Y
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: N318Y
| 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: 99.9%
- 3x: 99.7%
- 10x: 98.6%
- 20x: 93.1%
|
| 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: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 0610010F05Rik |
G |
T |
11: 23,576,764 (GRCm38) |
T696N |
probably benign |
Het |
| Ankrd45 |
T |
C |
1: 161,151,319 (GRCm38) |
|
probably null |
Het |
| Appl1 |
C |
A |
14: 26,927,794 (GRCm38) |
G592* |
probably null |
Het |
| Arfgef2 |
T |
A |
2: 166,878,544 (GRCm38) |
M1501K |
probably benign |
Het |
| Calcrl |
C |
T |
2: 84,339,339 (GRCm38) |
A333T |
probably damaging |
Het |
| Cd200r3 |
T |
A |
16: 44,951,472 (GRCm38) |
I33N |
probably benign |
Het |
| Ceacam15 |
A |
G |
7: 16,673,409 (GRCm38) |
L61P |
probably benign |
Het |
| Cfap69 |
T |
A |
5: 5,582,515 (GRCm38) |
H827L |
possibly damaging |
Het |
| Csmd3 |
T |
A |
15: 47,644,270 (GRCm38) |
E2780V |
probably damaging |
Het |
| Cyp2u1 |
G |
A |
3: 131,293,654 (GRCm38) |
T426I |
probably damaging |
Het |
| Eefsec |
A |
C |
6: 88,376,330 (GRCm38) |
I119S |
probably damaging |
Het |
| Fem1b |
T |
C |
9: 62,796,268 (GRCm38) |
N570S |
probably damaging |
Het |
| Fmo9 |
A |
G |
1: 166,663,526 (GRCm38) |
M461T |
probably benign |
Het |
| Fryl |
A |
G |
5: 73,133,277 (GRCm38) |
Y95H |
probably benign |
Het |
| Fsip2 |
T |
C |
2: 82,958,673 (GRCm38) |
I346T |
probably benign |
Het |
| Fto |
T |
C |
8: 91,485,190 (GRCm38) |
F381S |
probably damaging |
Het |
| Gabbr1 |
G |
C |
17: 37,048,583 (GRCm38) |
S150T |
probably benign |
Het |
| Galnt9 |
G |
T |
5: 110,615,473 (GRCm38) |
W448L |
probably damaging |
Het |
| Gcnt2 |
G |
T |
13: 40,917,722 (GRCm38) |
|
probably benign |
Het |
| Gm10800 |
CAAGAAAACTGAAAATCAAAGAAAACTGAAAATCA |
CAAGAAAACTGAAAATCA |
2: 98,667,016 (GRCm38) |
|
probably null |
Het |
| Gm17727 |
T |
C |
9: 35,778,033 (GRCm38) |
*84W |
probably null |
Het |
| Gm8882 |
C |
T |
6: 132,361,568 (GRCm38) |
G229D |
unknown |
Het |
| Gmcl1 |
G |
T |
6: 86,721,426 (GRCm38) |
A163E |
probably damaging |
Het |
| Hectd4 |
A |
G |
5: 121,332,949 (GRCm38) |
Y2633C |
possibly damaging |
Het |
| Hsd11b2 |
A |
G |
8: 105,522,634 (GRCm38) |
I214V |
probably damaging |
Het |
| Hspa12a |
T |
A |
19: 58,821,013 (GRCm38) |
E217V |
possibly damaging |
Het |
| Itih2 |
A |
G |
2: 10,097,137 (GRCm38) |
F845L |
probably damaging |
Het |
| Kcnn3 |
T |
A |
3: 89,661,233 (GRCm38) |
L606H |
probably damaging |
Het |
| Krt6b |
G |
A |
15: 101,680,142 (GRCm38) |
R28C |
probably damaging |
Het |
| Lama2 |
T |
A |
10: 26,990,870 (GRCm38) |
D2876V |
probably damaging |
Het |
| Lmbrd2 |
T |
C |
15: 9,175,192 (GRCm38) |
S397P |
probably damaging |
Het |
| Lmf2 |
C |
T |
15: 89,352,358 (GRCm38) |
|
probably null |
Het |
| Lrp2 |
A |
G |
2: 69,506,453 (GRCm38) |
I1325T |
probably benign |
Het |
| Ltbp2 |
A |
T |
12: 84,803,902 (GRCm38) |
C879* |
probably null |
Het |
| Map3k1 |
A |
G |
13: 111,755,313 (GRCm38) |
V1136A |
probably damaging |
Het |
| Mettl3 |
G |
T |
14: 52,300,252 (GRCm38) |
H84N |
probably benign |
Het |
| Mia2 |
A |
G |
12: 59,109,087 (GRCm38) |
|
probably null |
Het |
| Mlip |
G |
T |
9: 77,239,579 (GRCm38) |
T92K |
probably damaging |
Het |
| Nalcn |
T |
A |
14: 123,464,701 (GRCm38) |
Y466F |
probably benign |
Het |
| Nav2 |
T |
A |
7: 49,551,950 (GRCm38) |
L235* |
probably null |
Het |
| Nbn |
T |
C |
4: 15,981,588 (GRCm38) |
V560A |
probably benign |
Het |
| Ncln |
A |
T |
10: 81,493,153 (GRCm38) |
Y144N |
possibly damaging |
Het |
| Nfe2l2 |
A |
C |
2: 75,679,421 (GRCm38) |
D18E |
probably benign |
Het |
| Olfr102 |
A |
G |
17: 37,313,713 (GRCm38) |
F224L |
probably benign |
Het |
| Olfr1131 |
T |
C |
2: 87,628,607 (GRCm38) |
I48T |
possibly damaging |
Het |
| Olfr356 |
T |
C |
2: 36,937,709 (GRCm38) |
C197R |
possibly damaging |
Het |
| Olfr432 |
G |
A |
1: 174,050,525 (GRCm38) |
A51T |
probably benign |
Het |
| Otop3 |
A |
T |
11: 115,339,395 (GRCm38) |
M33L |
probably benign |
Het |
| Pdzd2 |
G |
A |
15: 12,373,506 (GRCm38) |
S2181L |
probably benign |
Het |
| Phf14 |
T |
C |
6: 11,953,423 (GRCm38) |
I387T |
possibly damaging |
Het |
| Proca1 |
A |
G |
11: 78,204,911 (GRCm38) |
D123G |
probably damaging |
Het |
| Prune2 |
G |
A |
19: 17,120,719 (GRCm38) |
G1196S |
probably benign |
Het |
| Psd3 |
T |
A |
8: 68,121,056 (GRCm38) |
S158C |
probably damaging |
Het |
| Rps18 |
A |
G |
17: 33,955,136 (GRCm38) |
V15A |
probably benign |
Het |
| Sharpin |
C |
A |
15: 76,347,765 (GRCm38) |
R271L |
possibly damaging |
Het |
| Smad5 |
C |
A |
13: 56,723,888 (GRCm38) |
Q99K |
probably damaging |
Het |
| Sox5 |
T |
C |
6: 144,116,474 (GRCm38) |
M151V |
possibly damaging |
Het |
| Sphkap |
A |
T |
1: 83,278,771 (GRCm38) |
F419Y |
possibly damaging |
Het |
| Tbx20 |
T |
A |
9: 24,725,525 (GRCm38) |
Y422F |
probably damaging |
Het |
| Tcirg1 |
A |
C |
19: 3,899,099 (GRCm38) |
F397V |
probably damaging |
Het |
| Tex36 |
G |
A |
7: 133,595,283 (GRCm38) |
S35F |
possibly damaging |
Het |
| Tsen54 |
G |
T |
11: 115,814,934 (GRCm38) |
A26S |
unknown |
Het |
| Usp50 |
T |
A |
2: 126,780,330 (GRCm38) |
|
probably null |
Het |
| Vmn2r5 |
A |
T |
3: 64,491,288 (GRCm38) |
F757I |
probably benign |
Het |
| Zbbx |
T |
C |
3: 75,155,442 (GRCm38) |
T3A |
possibly damaging |
Het |
| Zfp28 |
T |
A |
7: 6,389,829 (GRCm38) |
M168K |
probably benign |
Het |
| Zfp568 |
G |
T |
7: 30,023,126 (GRCm38) |
G499W |
probably damaging |
Het |
| Zfp7 |
C |
G |
15: 76,890,931 (GRCm38) |
P391R |
possibly damaging |
Het |
|
| Other mutations in Prdm9 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01302:Prdm9
|
APN |
17 |
15,553,346 (GRCm38) |
missense |
probably benign |
0.11 |
|
IGL02322:Prdm9
|
APN |
17 |
15,562,848 (GRCm38) |
missense |
probably damaging |
0.99 |
|
IGL02354:Prdm9
|
APN |
17 |
15,562,847 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL02361:Prdm9
|
APN |
17 |
15,562,847 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL02724:Prdm9
|
APN |
17 |
15,563,260 (GRCm38) |
missense |
probably benign |
0.07 |
|
IGL03120:Prdm9
|
APN |
17 |
15,544,931 (GRCm38) |
missense |
probably benign |
|
|
berlin
|
UTSW |
17 |
15,562,440 (GRCm38) |
missense |
probably damaging |
0.96 |
|
R0173:Prdm9
|
UTSW |
17 |
15,544,035 (GRCm38) |
missense |
probably benign |
0.00 |
|
R0173:Prdm9
|
UTSW |
17 |
15,544,013 (GRCm38) |
missense |
probably benign |
0.02 |
|
R0309:Prdm9
|
UTSW |
17 |
15,557,384 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R1420:Prdm9
|
UTSW |
17 |
15,544,376 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3498:Prdm9
|
UTSW |
17 |
15,562,945 (GRCm38) |
splice site |
probably benign |
|
|
R3714:Prdm9
|
UTSW |
17 |
15,557,361 (GRCm38) |
nonsense |
probably null |
|
|
R4118:Prdm9
|
UTSW |
17 |
15,544,013 (GRCm38) |
missense |
probably benign |
0.02 |
|
R4369:Prdm9
|
UTSW |
17 |
15,544,446 (GRCm38) |
missense |
probably benign |
0.14 |
|
R4691:Prdm9
|
UTSW |
17 |
15,553,378 (GRCm38) |
missense |
probably benign |
0.03 |
|
R4742:Prdm9
|
UTSW |
17 |
15,553,521 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R4910:Prdm9
|
UTSW |
17 |
15,544,323 (GRCm38) |
missense |
probably benign |
0.08 |
|
R5056:Prdm9
|
UTSW |
17 |
15,562,417 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
R5130:Prdm9
|
UTSW |
17 |
15,544,467 (GRCm38) |
missense |
probably benign |
0.00 |
|
R5175:Prdm9
|
UTSW |
17 |
15,557,451 (GRCm38) |
missense |
probably benign |
0.04 |
|
R5187:Prdm9
|
UTSW |
17 |
15,562,893 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R5213:Prdm9
|
UTSW |
17 |
15,555,154 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R5270:Prdm9
|
UTSW |
17 |
15,553,363 (GRCm38) |
missense |
probably benign |
0.16 |
|
R5635:Prdm9
|
UTSW |
17 |
15,562,440 (GRCm38) |
missense |
probably damaging |
0.96 |
|
R6753:Prdm9
|
UTSW |
17 |
15,544,956 (GRCm38) |
missense |
probably benign |
0.00 |
|
R6857:Prdm9
|
UTSW |
17 |
15,544,256 (GRCm38) |
missense |
probably benign |
0.04 |
|
R7041:Prdm9
|
UTSW |
17 |
15,544,995 (GRCm38) |
missense |
possibly damaging |
0.56 |
|
R7355:Prdm9
|
UTSW |
17 |
15,545,235 (GRCm38) |
missense |
probably benign |
0.01 |
|
R7410:Prdm9
|
UTSW |
17 |
15,544,997 (GRCm38) |
missense |
possibly damaging |
0.73 |
|
R7570:Prdm9
|
UTSW |
17 |
15,555,652 (GRCm38) |
missense |
probably benign |
0.14 |
|
R7571:Prdm9
|
UTSW |
17 |
15,563,264 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R7575:Prdm9
|
UTSW |
17 |
15,544,628 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7593:Prdm9
|
UTSW |
17 |
15,544,605 (GRCm38) |
missense |
possibly damaging |
0.81 |
|
R7664:Prdm9
|
UTSW |
17 |
15,555,571 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R7755:Prdm9
|
UTSW |
17 |
15,544,964 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7817:Prdm9
|
UTSW |
17 |
15,559,049 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7875:Prdm9
|
UTSW |
17 |
15,553,542 (GRCm38) |
nonsense |
probably null |
|
|
R8222:Prdm9
|
UTSW |
17 |
15,544,773 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
R8405:Prdm9
|
UTSW |
17 |
15,544,194 (GRCm38) |
missense |
probably benign |
0.22 |
|
R8695:Prdm9
|
UTSW |
17 |
15,544,757 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8947:Prdm9
|
UTSW |
17 |
15,544,008 (GRCm38) |
missense |
possibly damaging |
0.96 |
|
X0021:Prdm9
|
UTSW |
17 |
15,553,472 (GRCm38) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- CCCTCAGTATTCCAATTTTGCTGAG -3'
(R):5'- CATGATGACTCAGAAGCCTCATG -3'
Sequencing Primer
(F):5'- TCCAATTTTGCTGAGTAGATTTGTAC -3'
(R):5'- TCAGAAGCCTCATGTGCGGTC -3'
|
| Posted On |
2020-06-30 |
Incidental Mutation