Incidental Mutation 'IGL03120:Prdm9'
| ID |
409932 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Prdm9
|
| Ensembl Gene |
ENSMUSG00000051977 |
| Gene Name |
PR domain containing 9 |
| Synonyms |
Meisetz, repro7, Dsbc1, Rcr1, G1-419-29 |
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.351)
|
| Stock # |
IGL03120
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
17 |
| Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 15765193 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 529
(N529S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000131871
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000167994]
|
| AlphaFold |
Q96EQ9 |
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128267
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130297
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000167994
AA Change: N529S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: N529S
| 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
|
| 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: 32 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110059G10Rik |
A |
G |
9: 122,778,118 (GRCm39) |
L42P |
probably benign |
Het |
| Cacna1e |
T |
C |
1: 154,319,627 (GRCm39) |
I1420V |
probably damaging |
Het |
| Cemip2 |
G |
A |
19: 21,801,207 (GRCm39) |
D775N |
possibly damaging |
Het |
| Corin |
T |
C |
5: 72,518,032 (GRCm39) |
Y263C |
probably damaging |
Het |
| Cyp4f15 |
A |
T |
17: 32,909,738 (GRCm39) |
I112F |
probably damaging |
Het |
| Dach1 |
T |
C |
14: 98,065,225 (GRCm39) |
E724G |
probably damaging |
Het |
| Dip2b |
T |
C |
15: 100,101,008 (GRCm39) |
|
probably benign |
Het |
| Dnah2 |
T |
A |
11: 69,312,674 (GRCm39) |
E4297V |
probably damaging |
Het |
| Dot1l |
A |
G |
10: 80,622,107 (GRCm39) |
|
probably benign |
Het |
| Endod1 |
C |
A |
9: 14,268,331 (GRCm39) |
V385F |
probably damaging |
Het |
| Etnppl |
A |
G |
3: 130,414,341 (GRCm39) |
T73A |
probably damaging |
Het |
| Frmd4b |
T |
A |
6: 97,373,206 (GRCm39) |
D104V |
possibly damaging |
Het |
| Gp5 |
T |
C |
16: 30,127,016 (GRCm39) |
I553V |
possibly damaging |
Het |
| Gpc5 |
A |
G |
14: 115,607,556 (GRCm39) |
E386G |
possibly damaging |
Het |
| Hbb-bs |
A |
G |
7: 103,476,985 (GRCm39) |
|
probably benign |
Het |
| Klra2 |
T |
A |
6: 131,197,180 (GRCm39) |
Y273F |
probably benign |
Het |
| Lrrc37 |
T |
C |
11: 103,507,801 (GRCm39) |
|
probably benign |
Het |
| Msto1 |
A |
T |
3: 88,818,116 (GRCm39) |
V366E |
probably damaging |
Het |
| Mtcl1 |
A |
G |
17: 66,686,378 (GRCm39) |
S843P |
probably damaging |
Het |
| Nhsl2 |
A |
G |
X: 101,114,939 (GRCm39) |
N97S |
probably benign |
Het |
| Npm2 |
C |
A |
14: 70,890,039 (GRCm39) |
|
probably benign |
Het |
| Npr2 |
C |
T |
4: 43,643,133 (GRCm39) |
R506C |
probably damaging |
Het |
| Olr1 |
T |
C |
6: 129,465,898 (GRCm39) |
E36G |
probably damaging |
Het |
| Or56b2 |
A |
T |
7: 104,337,609 (GRCm39) |
Y129F |
probably benign |
Het |
| Pcdhb19 |
A |
G |
18: 37,631,209 (GRCm39) |
I335V |
probably benign |
Het |
| Pla2g6 |
T |
C |
15: 79,171,060 (GRCm39) |
D772G |
probably damaging |
Het |
| Ppfibp1 |
C |
A |
6: 146,899,667 (GRCm39) |
D119E |
probably benign |
Het |
| Rnf20 |
T |
A |
4: 49,649,955 (GRCm39) |
|
probably benign |
Het |
| Spata31h1 |
A |
G |
10: 82,120,869 (GRCm39) |
V77A |
possibly damaging |
Het |
| Tmem132c |
T |
A |
5: 127,640,448 (GRCm39) |
V873E |
probably benign |
Het |
| Ttn |
T |
C |
2: 76,757,428 (GRCm39) |
|
probably null |
Het |
| Vmn2r54 |
A |
G |
7: 12,349,314 (GRCm39) |
I756T |
probably damaging |
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 |
|
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 |
|
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 |
|
|
| Posted On |
2016-08-02 |
Incidental Mutation