Incidental Mutation 'R1083:Phf1'
ID |
84936 |
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 |
039169-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R1083 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
17 |
Chromosomal Location |
27152101-27156882 bp(+) (GRCm39) |
Type of Mutation |
unclassified |
DNA Base Change (assembly) |
T to C
at 27156244 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000155085
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025027]
[ENSMUST00000073724]
[ENSMUST00000078961]
[ENSMUST00000114935]
[ENSMUST00000177932]
[ENSMUST00000194598]
[ENSMUST00000229490]
[ENSMUST00000201702]
|
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 benign
Transcript: ENSMUST00000073724
|
SMART Domains |
Protein: ENSMUSP00000073402 Gene: ENSMUSG00000024193
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: ENSMUST00000229490
|
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 |
|
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.1%
- 20x: 94.0%
|
Validation Efficiency |
100% (38/38) |
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: 37 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A730049H05Rik |
T |
C |
6: 92,805,046 (GRCm39) |
|
probably benign |
Het |
Adamts17 |
G |
A |
7: 66,797,322 (GRCm39) |
C986Y |
probably damaging |
Het |
AI987944 |
A |
G |
7: 41,024,763 (GRCm39) |
V75A |
probably benign |
Het |
Arhgap10 |
T |
C |
8: 78,244,378 (GRCm39) |
Y12C |
probably damaging |
Het |
Atp11b |
G |
A |
3: 35,832,162 (GRCm39) |
|
probably benign |
Het |
Ccer1 |
T |
A |
10: 97,530,520 (GRCm39) |
D394E |
possibly damaging |
Het |
Cdh2 |
T |
C |
18: 16,777,016 (GRCm39) |
N273S |
possibly damaging |
Het |
Cfap65 |
G |
T |
1: 74,957,663 (GRCm39) |
|
probably benign |
Het |
Crybb3 |
A |
T |
5: 113,228,444 (GRCm39) |
|
probably benign |
Het |
D7Ertd443e |
G |
A |
7: 133,950,663 (GRCm39) |
Q337* |
probably null |
Het |
Dixdc1 |
C |
T |
9: 50,588,293 (GRCm39) |
|
probably benign |
Het |
Dut |
GCGGC |
GCGGCCGGC |
2: 125,089,748 (GRCm39) |
|
probably null |
Het |
Fbxo2 |
A |
G |
4: 148,250,234 (GRCm39) |
|
probably null |
Het |
Gm5174 |
T |
C |
10: 86,491,972 (GRCm39) |
|
noncoding transcript |
Het |
Gpam |
A |
G |
19: 55,076,643 (GRCm39) |
|
probably benign |
Het |
Il12a |
C |
T |
3: 68,602,666 (GRCm39) |
T112M |
probably damaging |
Het |
Itpr1 |
T |
A |
6: 108,487,657 (GRCm39) |
V2361D |
possibly damaging |
Het |
Jag1 |
G |
A |
2: 136,938,152 (GRCm39) |
L283F |
probably damaging |
Het |
Lamb2 |
A |
C |
9: 108,360,892 (GRCm39) |
D538A |
probably benign |
Het |
Map10 |
T |
A |
8: 126,397,178 (GRCm39) |
C190* |
probably null |
Het |
Pcnx2 |
C |
T |
8: 126,498,843 (GRCm39) |
R1552H |
probably damaging |
Het |
Pitx2 |
A |
G |
3: 129,012,418 (GRCm39) |
T276A |
probably damaging |
Het |
Pparg |
A |
G |
6: 115,467,107 (GRCm39) |
D490G |
probably damaging |
Het |
Rnf10 |
A |
T |
5: 115,398,163 (GRCm39) |
|
probably benign |
Het |
Sbp |
T |
C |
17: 24,161,704 (GRCm39) |
|
probably benign |
Het |
Setbp1 |
A |
T |
18: 78,900,841 (GRCm39) |
L942H |
probably damaging |
Het |
Sf3b1 |
C |
G |
1: 55,058,554 (GRCm39) |
E12Q |
possibly damaging |
Het |
Sfmbt1 |
A |
T |
14: 30,509,498 (GRCm39) |
N326Y |
possibly damaging |
Het |
Slx4 |
G |
A |
16: 3,808,774 (GRCm39) |
Q389* |
probably null |
Het |
Srrm3 |
T |
A |
5: 135,883,263 (GRCm39) |
V206E |
probably damaging |
Het |
Sspo |
T |
A |
6: 48,447,933 (GRCm39) |
D2270E |
possibly damaging |
Het |
Sulf1 |
AAGGGA |
AAGGGAGGGA |
1: 12,906,388 (GRCm39) |
|
probably null |
Het |
Vmn1r14 |
T |
A |
6: 57,211,184 (GRCm39) |
I210N |
probably damaging |
Het |
Wasf3 |
T |
G |
5: 146,372,182 (GRCm39) |
L13R |
probably damaging |
Het |
Yes1 |
T |
C |
5: 32,809,101 (GRCm39) |
|
probably null |
Het |
Zfp292 |
T |
C |
4: 34,807,569 (GRCm39) |
D1830G |
probably damaging |
Het |
Zfp541 |
A |
G |
7: 15,812,637 (GRCm39) |
N430S |
probably benign |
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 |
R1537:Phf1
|
UTSW |
17 |
27,154,372 (GRCm39) |
critical splice donor site |
probably null |
|
R1587:Phf1
|
UTSW |
17 |
27,156,466 (GRCm39) |
missense |
probably damaging |
0.99 |
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'- TGTGGATTGTTGTCCCAAAGAGCTG -3'
(R):5'- AACTAGGTACTGCACAGAGCCGTC -3'
Sequencing Primer
(F):5'- CTCTACCCAGCTTTGAGTATGTGAG -3'
(R):5'- GCACTCTTCGAGCAAGGAC -3'
|
Posted On |
2013-11-18 |