Incidental Mutation 'R1587:Phf1'
| ID |
177602 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Phf1
|
| Ensembl Gene |
ENSMUSG00000024193 |
| Gene Name |
PHD finger protein 1 |
| Synonyms |
PHF2, Tctex3, Tctex-3, D17Ertd455e, mPcl1 |
| MMRRC Submission |
039624-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R1587 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
27152101-27156882 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 27156466 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Aspartic acid
at position 536
(V536D)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000073402
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025027]
[ENSMUST00000073724]
[ENSMUST00000078961]
[ENSMUST00000114935]
[ENSMUST00000177932]
[ENSMUST00000194598]
[ENSMUST00000201702]
[ENSMUST00000229490]
|
| AlphaFold |
Q9Z1B8 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025027
|
| SMART Domains |
Protein: ENSMUSP00000025027
Gene: ENSMUSG00000024194
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
7 |
29 |
N/A |
INTRINSIC |
|
low complexity region
|
45 |
60 |
N/A |
INTRINSIC |
|
Pfam:CutA1
|
67 |
165 |
6.9e-44 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000073724
AA Change: V536D
PolyPhen 2
Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000073402
Gene: ENSMUSG00000024193
AA Change: V536D
| Domain | Start | End | E-Value | Type |
|---|
|
TUDOR
|
29 |
86 |
5.61e-11 |
SMART |
|
PHD
|
89 |
140 |
2.81e-8 |
SMART |
|
PHD
|
188 |
238 |
2.42e0 |
SMART |
|
low complexity region
|
410 |
416 |
N/A |
INTRINSIC |
|
low complexity region
|
481 |
495 |
N/A |
INTRINSIC |
|
Pfam:Mtf2_C
|
523 |
557 |
7.7e-11 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000078961
|
| SMART Domains |
Protein: ENSMUSP00000077984
Gene: ENSMUSG00000024301
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
25 |
36 |
N/A |
INTRINSIC |
|
low complexity region
|
108 |
117 |
N/A |
INTRINSIC |
|
low complexity region
|
222 |
240 |
N/A |
INTRINSIC |
|
KISc
|
307 |
670 |
1.34e-143 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114935
|
| SMART Domains |
Protein: ENSMUSP00000110585
Gene: ENSMUSG00000024194
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Pfam:CutA1
|
43 |
144 |
1.7e-44 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177932
|
| SMART Domains |
Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
27 |
253 |
3.23e-8 |
SMART |
|
C2
|
263 |
362 |
7.4e-10 |
SMART |
|
RasGAP
|
392 |
729 |
3.33e-118 |
SMART |
|
low complexity region
|
787 |
803 |
N/A |
INTRINSIC |
|
low complexity region
|
938 |
973 |
N/A |
INTRINSIC |
|
low complexity region
|
1040 |
1068 |
N/A |
INTRINSIC |
|
low complexity region
|
1110 |
1125 |
N/A |
INTRINSIC |
|
coiled coil region
|
1186 |
1259 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184739
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000193200
|
| SMART Domains |
Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
12 |
238 |
1.5e-10 |
SMART |
|
C2
|
248 |
347 |
4.8e-12 |
SMART |
|
RasGAP
|
377 |
714 |
2.1e-120 |
SMART |
|
low complexity region
|
772 |
788 |
N/A |
INTRINSIC |
|
low complexity region
|
923 |
958 |
N/A |
INTRINSIC |
|
low complexity region
|
1025 |
1053 |
N/A |
INTRINSIC |
|
low complexity region
|
1095 |
1110 |
N/A |
INTRINSIC |
|
coiled coil region
|
1171 |
1244 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194598
|
| SMART Domains |
Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
27 |
253 |
3.23e-8 |
SMART |
|
C2
|
263 |
362 |
7.4e-10 |
SMART |
|
RasGAP
|
392 |
729 |
3.33e-118 |
SMART |
|
low complexity region
|
787 |
803 |
N/A |
INTRINSIC |
|
low complexity region
|
938 |
973 |
N/A |
INTRINSIC |
|
low complexity region
|
1040 |
1068 |
N/A |
INTRINSIC |
|
low complexity region
|
1110 |
1125 |
N/A |
INTRINSIC |
|
coiled coil region
|
1186 |
1259 |
N/A |
INTRINSIC |
|
low complexity region
|
1308 |
1326 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000201349
|
| SMART Domains |
Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
| Domain | Start | End | E-Value | Type |
|---|
|
RasGAP
|
9 |
346 |
2.2e-120 |
SMART |
|
low complexity region
|
404 |
420 |
N/A |
INTRINSIC |
|
low complexity region
|
555 |
590 |
N/A |
INTRINSIC |
|
low complexity region
|
657 |
685 |
N/A |
INTRINSIC |
|
low complexity region
|
727 |
742 |
N/A |
INTRINSIC |
|
Blast:RasGAP
|
761 |
876 |
3e-21 |
BLAST |
|
low complexity region
|
884 |
894 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000201702
|
| SMART Domains |
Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
27 |
253 |
1.5e-10 |
SMART |
|
C2
|
263 |
362 |
4.9e-12 |
SMART |
|
RasGAP
|
392 |
729 |
2.2e-120 |
SMART |
|
low complexity region
|
773 |
789 |
N/A |
INTRINSIC |
|
low complexity region
|
924 |
959 |
N/A |
INTRINSIC |
|
low complexity region
|
1026 |
1054 |
N/A |
INTRINSIC |
|
low complexity region
|
1096 |
1111 |
N/A |
INTRINSIC |
|
coiled coil region
|
1171 |
1243 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000229490
|
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.0%
- 10x: 95.2%
- 20x: 88.9%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: The protein encoded by this gene belongs to the polycomb-like protein family, which is a component of polycomb repressive complex-2. This complex represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 and is required for the regulation of developmental genes including homeotic genes. The gene is expressed primarily in testis tissue. Small interfering RNA-mediated knockdown in cultured cell lines results in changes in homeotic gene expression coincident with alterations in promoter methylation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A530064D06Rik |
A |
T |
17: 48,473,585 (GRCm39) |
S111T |
probably benign |
Het |
| Abhd2 |
A |
T |
7: 79,003,758 (GRCm39) |
H279L |
probably benign |
Het |
| Ablim1 |
C |
T |
19: 57,071,979 (GRCm39) |
M1I |
probably null |
Het |
| Agrn |
T |
C |
4: 156,263,897 (GRCm39) |
Q122R |
probably damaging |
Het |
| Arfgef1 |
A |
T |
1: 10,230,184 (GRCm39) |
F1218I |
probably damaging |
Het |
| Bud13 |
C |
T |
9: 46,201,513 (GRCm39) |
P395S |
probably damaging |
Het |
| Ccdc110 |
G |
A |
8: 46,394,783 (GRCm39) |
V225M |
probably benign |
Het |
| Ccdc30 |
A |
T |
4: 119,210,373 (GRCm39) |
S248T |
probably damaging |
Het |
| Cdh20 |
C |
A |
1: 110,027,757 (GRCm39) |
Q501K |
probably damaging |
Het |
| Cwc27 |
T |
C |
13: 104,929,145 (GRCm39) |
D266G |
probably benign |
Het |
| Cyp2d40 |
T |
A |
15: 82,645,334 (GRCm39) |
|
probably null |
Het |
| Cyp4a32 |
T |
G |
4: 115,467,731 (GRCm39) |
N238K |
probably benign |
Het |
| Ddx11 |
T |
C |
17: 66,456,251 (GRCm39) |
L770P |
probably damaging |
Het |
| Dgcr8 |
C |
T |
16: 18,098,155 (GRCm39) |
G412E |
probably damaging |
Het |
| Disp2 |
C |
A |
2: 118,622,064 (GRCm39) |
A932D |
probably damaging |
Het |
| Dlg4 |
T |
A |
11: 69,922,572 (GRCm39) |
N291K |
possibly damaging |
Het |
| Dnajc7 |
A |
G |
11: 100,492,556 (GRCm39) |
I39T |
probably damaging |
Het |
| Elp1 |
G |
A |
4: 56,786,666 (GRCm39) |
Q426* |
probably null |
Het |
| Eno3 |
T |
C |
11: 70,552,296 (GRCm39) |
V316A |
probably damaging |
Het |
| Ep400 |
G |
A |
5: 110,874,768 (GRCm39) |
T944I |
probably benign |
Het |
| Ezh2 |
T |
G |
6: 47,529,424 (GRCm39) |
|
probably null |
Het |
| F7 |
A |
T |
8: 13,084,783 (GRCm39) |
I270F |
possibly damaging |
Het |
| Fancc |
A |
G |
13: 63,488,246 (GRCm39) |
F245L |
probably benign |
Het |
| Fzd7 |
G |
A |
1: 59,522,165 (GRCm39) |
C16Y |
possibly damaging |
Het |
| Gm29394 |
A |
G |
15: 57,892,008 (GRCm39) |
*200Q |
probably null |
Het |
| Ints8 |
A |
G |
4: 11,245,722 (GRCm39) |
|
probably null |
Het |
| Krt36 |
A |
T |
11: 99,993,128 (GRCm39) |
I449N |
probably damaging |
Het |
| Ldlr |
A |
T |
9: 21,649,209 (GRCm39) |
H328L |
probably damaging |
Het |
| Limk2 |
T |
C |
11: 3,303,455 (GRCm39) |
N101S |
possibly damaging |
Het |
| Lrp4 |
A |
G |
2: 91,306,650 (GRCm39) |
N321S |
probably benign |
Het |
| Mafk |
T |
C |
5: 139,785,900 (GRCm39) |
S33P |
probably damaging |
Het |
| Mbtps1 |
T |
C |
8: 120,244,958 (GRCm39) |
Y831C |
probably damaging |
Het |
| Mfge8 |
T |
A |
7: 78,784,513 (GRCm39) |
I344F |
probably damaging |
Het |
| Myo5b |
T |
C |
18: 74,867,061 (GRCm39) |
V1430A |
probably benign |
Het |
| Nbas |
G |
A |
12: 13,608,686 (GRCm39) |
R2154H |
probably benign |
Het |
| Nlrp6 |
G |
A |
7: 140,502,959 (GRCm39) |
R355H |
probably damaging |
Het |
| Noc4l |
T |
C |
5: 110,800,889 (GRCm39) |
T76A |
probably benign |
Het |
| Nrp1 |
T |
A |
8: 129,202,763 (GRCm39) |
C583S |
probably damaging |
Het |
| Or2w4 |
C |
T |
13: 21,796,083 (GRCm39) |
D19N |
probably benign |
Het |
| Or5d35 |
T |
A |
2: 87,855,477 (GRCm39) |
M137K |
probably damaging |
Het |
| Pgm5 |
T |
A |
19: 24,793,113 (GRCm39) |
I318F |
probably damaging |
Het |
| Prpf4b |
C |
A |
13: 35,076,133 (GRCm39) |
A641D |
probably benign |
Het |
| Ptpro |
T |
A |
6: 137,420,592 (GRCm39) |
V1007D |
probably damaging |
Het |
| Rbm47 |
A |
G |
5: 66,182,334 (GRCm39) |
I433T |
probably benign |
Het |
| Resf1 |
G |
T |
6: 149,228,018 (GRCm39) |
V355F |
probably damaging |
Het |
| S100a3 |
G |
A |
3: 90,509,618 (GRCm39) |
E88K |
probably benign |
Het |
| Sesn1 |
A |
G |
10: 41,687,108 (GRCm39) |
I31V |
probably benign |
Het |
| Son |
T |
A |
16: 91,456,606 (GRCm39) |
S1784R |
probably damaging |
Het |
| Srbd1 |
G |
T |
17: 86,292,865 (GRCm39) |
D901E |
probably damaging |
Het |
| St8sia6 |
C |
T |
2: 13,677,416 (GRCm39) |
D134N |
possibly damaging |
Het |
| Synpo2 |
T |
A |
3: 122,908,047 (GRCm39) |
D423V |
probably damaging |
Het |
| Vmn2r108 |
A |
G |
17: 20,692,383 (GRCm39) |
S158P |
probably damaging |
Het |
| Vmn2r109 |
A |
T |
17: 20,761,002 (GRCm39) |
V785E |
probably damaging |
Het |
| Zfp143 |
A |
G |
7: 109,673,275 (GRCm39) |
D124G |
probably benign |
Het |
| Zfp251 |
A |
G |
15: 76,754,484 (GRCm39) |
L54P |
probably damaging |
Het |
| Zfp324 |
G |
T |
7: 12,704,570 (GRCm39) |
S253I |
possibly damaging |
Het |
| Zfp59 |
A |
G |
7: 27,553,559 (GRCm39) |
E337G |
possibly damaging |
Het |
| Zfp663 |
G |
T |
2: 165,195,437 (GRCm39) |
Q261K |
probably benign |
Het |
| Zhx3 |
T |
C |
2: 160,623,613 (GRCm39) |
|
probably null |
Het |
|
| Other mutations in Phf1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00905:Phf1
|
APN |
17 |
27,155,568 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
IGL01629:Phf1
|
APN |
17 |
27,153,247 (GRCm39) |
missense |
probably benign |
0.07 |
|
IGL01931:Phf1
|
APN |
17 |
27,154,509 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02008:Phf1
|
APN |
17 |
27,154,260 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL02048:Phf1
|
APN |
17 |
27,153,515 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02206:Phf1
|
APN |
17 |
27,155,843 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02252:Phf1
|
APN |
17 |
27,154,109 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
IGL02548:Phf1
|
APN |
17 |
27,154,600 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03145:Phf1
|
APN |
17 |
27,153,344 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0539:Phf1
|
UTSW |
17 |
27,153,432 (GRCm39) |
splice site |
probably null |
|
|
R0815:Phf1
|
UTSW |
17 |
27,156,114 (GRCm39) |
unclassified |
probably benign |
|
|
R0863:Phf1
|
UTSW |
17 |
27,156,114 (GRCm39) |
unclassified |
probably benign |
|
|
R1028:Phf1
|
UTSW |
17 |
27,153,307 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R1083:Phf1
|
UTSW |
17 |
27,156,244 (GRCm39) |
unclassified |
probably benign |
|
|
R1537:Phf1
|
UTSW |
17 |
27,154,372 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1656:Phf1
|
UTSW |
17 |
27,156,333 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R1956:Phf1
|
UTSW |
17 |
27,154,719 (GRCm39) |
splice site |
probably null |
|
|
R2566:Phf1
|
UTSW |
17 |
27,156,062 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3196:Phf1
|
UTSW |
17 |
27,153,429 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4223:Phf1
|
UTSW |
17 |
27,156,474 (GRCm39) |
nonsense |
probably null |
|
|
R4835:Phf1
|
UTSW |
17 |
27,153,652 (GRCm39) |
missense |
probably benign |
|
|
R6439:Phf1
|
UTSW |
17 |
27,155,586 (GRCm39) |
missense |
probably benign |
|
|
R7070:Phf1
|
UTSW |
17 |
27,153,307 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R7289:Phf1
|
UTSW |
17 |
27,154,289 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7846:Phf1
|
UTSW |
17 |
27,154,291 (GRCm39) |
nonsense |
probably null |
|
|
R8165:Phf1
|
UTSW |
17 |
27,156,044 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R9645:Phf1
|
UTSW |
17 |
27,154,130 (GRCm39) |
critical splice donor site |
probably null |
|
|
X0028:Phf1
|
UTSW |
17 |
27,155,162 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGAAGCCCAGACTAGCATCAGTCC -3'
(R):5'- ATCGAGAGCGCCTCTTGTCAATC -3'
Sequencing Primer
(F):5'- ACCTCTGGGACTTCACATTGG -3'
(R):5'- GCATGAAAGTGCCAGTGTGT -3'
|
| Posted On |
2014-04-24 |
Incidental Mutation