Mutagenetix > Incidental Mutation

Incidental Mutation 'R0036:Phrf1'

64613

Institutional Source

Beutler Lab

Gene Symbol

Phrf1

Ensembl Gene

ENSMUSG00000038611

Gene Name

PHD and ring finger domains 1

Synonyms

MMRRC Submission

038330-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0036 (G1)

Quality Score

115

Status

Validated

Chromosome

Chromosomal Location

140808697-140842663 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 140841693 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 1435 (M1435T)

Ref Sequence

ENSEMBL: ENSMUSP00000113195 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026571] [ENSMUST00000097952] [ENSMUST00000106023] [ENSMUST00000106027] [ENSMUST00000122143] [ENSMUST00000132540] [ENSMUST00000209899] [ENSMUST00000155123]

AlphaFold

A6H619

Predicted Effect

probably benign
Transcript: ENSMUST00000026571

SMART Domains

Protein: ENSMUSP00000026571
Gene: ENSMUSG00000025498

Domain	Start	End	E-Value	Type
IRF	5	127	1.13e-54	SMART
IRF-3	240	420	1.38e-63	SMART
low complexity region	425	442	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000097952

SMART Domains

Protein: ENSMUSP00000095565
Gene: ENSMUSG00000025498

Domain	Start	End	E-Value	Type
IRF	5	127	1.13e-54	SMART
IRF-3	209	389	1.38e-63	SMART
low complexity region	394	411	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106023

SMART Domains

Protein: ENSMUSP00000101644
Gene: ENSMUSG00000025498

Domain	Start	End	E-Value	Type
IRF	5	127	1.13e-54	SMART
IRF-3	208	388	1.38e-63	SMART
low complexity region	393	410	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000106027
AA Change: M1594T

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000101648
Gene: ENSMUSG00000038611
AA Change: M1594T

Domain	Start	End	E-Value	Type
low complexity region	24	35	N/A	INTRINSIC
low complexity region	39	70	N/A	INTRINSIC
RING	109	149	3.78e-5	SMART
C1	173	229	7.05e-2	SMART
PHD	187	233	1.77e-14	SMART
RING	188	232	3.17e0	SMART
low complexity region	332	369	N/A	INTRINSIC
low complexity region	491	505	N/A	INTRINSIC
low complexity region	507	522	N/A	INTRINSIC
low complexity region	717	728	N/A	INTRINSIC
low complexity region	831	857	N/A	INTRINSIC
low complexity region	891	902	N/A	INTRINSIC
low complexity region	944	955	N/A	INTRINSIC
low complexity region	965	976	N/A	INTRINSIC
low complexity region	999	1020	N/A	INTRINSIC
low complexity region	1027	1043	N/A	INTRINSIC
low complexity region	1051	1090	N/A	INTRINSIC
low complexity region	1094	1151	N/A	INTRINSIC
low complexity region	1160	1173	N/A	INTRINSIC
low complexity region	1217	1241	N/A	INTRINSIC
low complexity region	1245	1261	N/A	INTRINSIC
low complexity region	1288	1306	N/A	INTRINSIC
low complexity region	1308	1319	N/A	INTRINSIC
low complexity region	1359	1376	N/A	INTRINSIC
low complexity region	1426	1441	N/A	INTRINSIC
low complexity region	1575	1592	N/A	INTRINSIC
Blast:IG_like	1593	1636	4e-14	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000122143
AA Change: M1435T

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000113195
Gene: ENSMUSG00000038611
AA Change: M1435T

Domain	Start	End	E-Value	Type
C1	14	70	7.05e-2	SMART
PHD	28	74	1.77e-14	SMART
low complexity region	173	210	N/A	INTRINSIC
low complexity region	332	346	N/A	INTRINSIC
low complexity region	348	363	N/A	INTRINSIC
low complexity region	558	569	N/A	INTRINSIC
low complexity region	672	698	N/A	INTRINSIC
low complexity region	732	743	N/A	INTRINSIC
low complexity region	785	796	N/A	INTRINSIC
low complexity region	806	817	N/A	INTRINSIC
low complexity region	840	861	N/A	INTRINSIC
low complexity region	868	884	N/A	INTRINSIC
low complexity region	892	931	N/A	INTRINSIC
low complexity region	935	992	N/A	INTRINSIC
low complexity region	1001	1014	N/A	INTRINSIC
low complexity region	1058	1082	N/A	INTRINSIC
low complexity region	1086	1102	N/A	INTRINSIC
low complexity region	1129	1147	N/A	INTRINSIC
low complexity region	1149	1160	N/A	INTRINSIC
low complexity region	1200	1217	N/A	INTRINSIC
low complexity region	1267	1282	N/A	INTRINSIC
low complexity region	1416	1433	N/A	INTRINSIC
Blast:IG_like	1434	1477	4e-14	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000122868

Predicted Effect

probably benign
Transcript: ENSMUST00000123525

SMART Domains

Protein: ENSMUSP00000121026
Gene: ENSMUSG00000025498

Domain	Start	End	E-Value	Type
IRF	1	69	6.35e-3	SMART
IRF-3	77	251	2.62e-55	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000130687
AA Change: M242T

SMART Domains

Protein: ENSMUSP00000123351
Gene: ENSMUSG00000038611
AA Change: M242T

Domain	Start	End	E-Value	Type
low complexity region	33	50	N/A	INTRINSIC
low complexity region	100	115	N/A	INTRINSIC
low complexity region	224	241	N/A	INTRINSIC
Blast:IG_like	242	285	5e-15	BLAST

Predicted Effect

unknown
Transcript: ENSMUST00000142572
AA Change: M684T

SMART Domains

Protein: ENSMUSP00000117393
Gene: ENSMUSG00000038611
AA Change: M684T

Domain	Start	End	E-Value	Type
low complexity region	20	31	N/A	INTRINSIC
low complexity region	41	52	N/A	INTRINSIC
low complexity region	75	96	N/A	INTRINSIC
low complexity region	103	119	N/A	INTRINSIC
low complexity region	127	166	N/A	INTRINSIC
low complexity region	170	227	N/A	INTRINSIC
low complexity region	236	249	N/A	INTRINSIC
low complexity region	293	317	N/A	INTRINSIC
low complexity region	321	337	N/A	INTRINSIC
low complexity region	364	382	N/A	INTRINSIC
low complexity region	384	395	N/A	INTRINSIC
low complexity region	435	452	N/A	INTRINSIC
low complexity region	666	683	N/A	INTRINSIC
Blast:IG_like	684	727	3e-14	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144250

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156938

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131399

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148414

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127161

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146373

Predicted Effect

probably benign
Transcript: ENSMUST00000132540

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155744

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000210506

Predicted Effect

probably benign
Transcript: ENSMUST00000209899

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127223

Predicted Effect

probably benign
Transcript: ENSMUST00000155123

SMART Domains

Protein: ENSMUSP00000120759
Gene: ENSMUSG00000038611

Domain	Start	End	E-Value	Type
low complexity region	24	35	N/A	INTRINSIC
low complexity region	39	70	N/A	INTRINSIC
RING	109	149	3.78e-5	SMART
Blast:C1	165	209	2e-17	BLAST

Meta Mutation Damage Score

0.1000

Coding Region Coverage

1x: 99.3%
3x: 98.9%
10x: 97.7%
20x: 96.0%

Validation Efficiency

97% (33/34)

Allele List at MGI

Other mutations in this stock

Total: 15 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ctsq	C	T	13: 61,185,485 (GRCm39)		probably null	Het
Egln3	A	T	12: 54,232,378 (GRCm39)	D142E	possibly damaging	Het
Fam120a	G	A	13: 49,042,740 (GRCm39)		probably benign	Het
Hspg2	A	G	4: 137,270,160 (GRCm39)	T2373A	probably damaging	Het
Pcyox1l	G	T	18: 61,830,492 (GRCm39)	T460K	probably benign	Het
Rnf157	A	G	11: 116,287,128 (GRCm39)	Y32H	probably damaging	Het
Rnf224	C	T	2: 25,126,143 (GRCm39)	R70Q	probably damaging	Het
Rusc2	C	A	4: 43,424,009 (GRCm39)	D1054E	probably damaging	Het
S100a16	T	A	3: 90,449,763 (GRCm39)	M82K	probably benign	Het
Serpina3j	A	G	12: 104,283,606 (GRCm39)	T235A	probably benign	Het
Sgo2a	T	C	1: 58,054,787 (GRCm39)	S324P	probably benign	Het
Slf1	G	T	13: 77,249,070 (GRCm39)	Q373K	probably benign	Het
Son	T	A	16: 91,457,054 (GRCm39)		probably benign	Het
Tril	C	T	6: 53,795,618 (GRCm39)	A535T	probably benign	Het
Vipr1	G	A	9: 121,490,049 (GRCm39)	D141N	probably benign	Het

Other mutations in Phrf1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00551:Phrf1	APN	7	140,838,790 (GRCm39)	unclassified	probably benign
IGL01391:Phrf1	APN	7	140,842,394 (GRCm39)	missense	probably damaging	1.00
IGL01472:Phrf1	APN	7	140,836,403 (GRCm39)	splice site	probably benign
IGL01633:Phrf1	APN	7	140,840,413 (GRCm39)	missense	probably benign	0.43
IGL01808:Phrf1	APN	7	140,840,879 (GRCm39)	missense	probably damaging	1.00
IGL02004:Phrf1	APN	7	140,840,246 (GRCm39)	missense	probably benign	0.39
IGL02138:Phrf1	APN	7	140,839,196 (GRCm39)	unclassified	probably benign
IGL02678:Phrf1	APN	7	140,840,195 (GRCm39)	missense	probably damaging	1.00
IGL03077:Phrf1	APN	7	140,834,881 (GRCm39)	nonsense	probably null
PIT4466001:Phrf1	UTSW	7	140,838,725 (GRCm39)	missense	unknown
R0036:Phrf1	UTSW	7	140,841,693 (GRCm39)	missense	probably damaging	1.00
R0040:Phrf1	UTSW	7	140,823,770 (GRCm39)	missense	probably damaging	1.00
R0358:Phrf1	UTSW	7	140,838,217 (GRCm39)	unclassified	probably benign
R0445:Phrf1	UTSW	7	140,827,244 (GRCm39)	utr 3 prime	probably benign
R0535:Phrf1	UTSW	7	140,839,978 (GRCm39)	missense	probably benign	0.07
R0561:Phrf1	UTSW	7	140,834,876 (GRCm39)	missense	probably benign	0.00
R0940:Phrf1	UTSW	7	140,834,768 (GRCm39)	splice site	probably benign
R1499:Phrf1	UTSW	7	140,836,564 (GRCm39)	missense	probably damaging	1.00
R1511:Phrf1	UTSW	7	140,839,714 (GRCm39)	unclassified	probably benign
R1651:Phrf1	UTSW	7	140,817,434 (GRCm39)	missense	probably benign
R1691:Phrf1	UTSW	7	140,841,787 (GRCm39)	nonsense	probably null
R1778:Phrf1	UTSW	7	140,812,369 (GRCm39)	missense	probably benign	0.01
R1851:Phrf1	UTSW	7	140,820,831 (GRCm39)	missense	probably damaging	1.00
R2239:Phrf1	UTSW	7	140,817,605 (GRCm39)	missense	probably damaging	1.00
R2857:Phrf1	UTSW	7	140,839,593 (GRCm39)	unclassified	probably benign
R3796:Phrf1	UTSW	7	140,839,831 (GRCm39)	nonsense	probably null
R3797:Phrf1	UTSW	7	140,839,831 (GRCm39)	nonsense	probably null
R3798:Phrf1	UTSW	7	140,839,831 (GRCm39)	nonsense	probably null
R3799:Phrf1	UTSW	7	140,839,831 (GRCm39)	nonsense	probably null
R4080:Phrf1	UTSW	7	140,839,633 (GRCm39)	unclassified	probably benign
R4081:Phrf1	UTSW	7	140,838,970 (GRCm39)	unclassified	probably benign
R4557:Phrf1	UTSW	7	140,838,842 (GRCm39)	unclassified	probably benign
R5217:Phrf1	UTSW	7	140,840,616 (GRCm39)	missense	probably damaging	1.00
R5218:Phrf1	UTSW	7	140,841,214 (GRCm39)	missense	possibly damaging	0.94
R5276:Phrf1	UTSW	7	140,839,196 (GRCm39)	unclassified	probably benign
R5442:Phrf1	UTSW	7	140,820,850 (GRCm39)	missense	probably damaging	1.00
R5501:Phrf1	UTSW	7	140,839,834 (GRCm39)	missense	possibly damaging	0.91
R5695:Phrf1	UTSW	7	140,838,378 (GRCm39)	unclassified	probably benign
R5837:Phrf1	UTSW	7	140,839,974 (GRCm39)	missense	probably benign	0.34
R5907:Phrf1	UTSW	7	140,840,453 (GRCm39)	missense	possibly damaging	0.79
R5996:Phrf1	UTSW	7	140,839,015 (GRCm39)	unclassified	probably benign
R6024:Phrf1	UTSW	7	140,838,898 (GRCm39)	unclassified	probably benign
R6244:Phrf1	UTSW	7	140,817,586 (GRCm39)	missense	probably damaging	1.00
R6512:Phrf1	UTSW	7	140,840,309 (GRCm39)	missense	possibly damaging	0.88
R7016:Phrf1	UTSW	7	140,817,476 (GRCm39)	missense	probably damaging	0.98
R7311:Phrf1	UTSW	7	140,820,846 (GRCm39)	missense	unknown
R7409:Phrf1	UTSW	7	140,839,205 (GRCm39)	missense	unknown
R7517:Phrf1	UTSW	7	140,836,523 (GRCm39)	missense	unknown
R7560:Phrf1	UTSW	7	140,811,138 (GRCm39)	critical splice acceptor site	probably null
R7699:Phrf1	UTSW	7	140,834,842 (GRCm39)	missense	unknown
R7700:Phrf1	UTSW	7	140,834,842 (GRCm39)	missense	unknown
R7867:Phrf1	UTSW	7	140,836,524 (GRCm39)	missense	unknown
R7895:Phrf1	UTSW	7	140,839,288 (GRCm39)	missense	unknown
R8179:Phrf1	UTSW	7	140,836,493 (GRCm39)	missense	unknown
R8705:Phrf1	UTSW	7	140,838,651 (GRCm39)	missense	unknown
R8708:Phrf1	UTSW	7	140,812,446 (GRCm39)	missense	unknown
R8748:Phrf1	UTSW	7	140,838,148 (GRCm39)	missense	unknown
R8768:Phrf1	UTSW	7	140,838,651 (GRCm39)	missense	unknown
R8789:Phrf1	UTSW	7	140,836,581 (GRCm39)	missense	unknown
R8859:Phrf1	UTSW	7	140,836,516 (GRCm39)	missense	unknown
R8991:Phrf1	UTSW	7	140,823,671 (GRCm39)	missense	unknown
R9086:Phrf1	UTSW	7	140,839,412 (GRCm39)	missense	unknown
R9158:Phrf1	UTSW	7	140,836,466 (GRCm39)	missense	unknown
R9287:Phrf1	UTSW	7	140,840,055 (GRCm39)	missense	probably benign	0.35
R9561:Phrf1	UTSW	7	140,834,815 (GRCm39)	missense	unknown
X0027:Phrf1	UTSW	7	140,836,481 (GRCm39)	missense	probably benign
Z1176:Phrf1	UTSW	7	140,838,731 (GRCm39)	missense	unknown
Z1176:Phrf1	UTSW	7	140,823,796 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- CAATGCCAGCTACAGTCTCAGAGC -3'
(R):5'- TGTCACAATGTGTCCCTTGCAACC -3'

Sequencing Primer
(F):5'- CCTGATTTTAGGTAGAGTATCCAGGC -3'
(R):5'- GTCCCTTGCAACCTCAGAG -3'

Posted On

2013-08-06