Mutagenetix > Incidental Mutation

Incidental Mutation 'R4926:Prpf39'

379054

Institutional Source

Beutler Lab

Gene Symbol

Prpf39

Ensembl Gene

ENSMUSG00000035597

Gene Name

pre-mRNA processing factor 39

Synonyms

Srcs1

MMRRC Submission

042527-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.947) question?

Stock #

R4926 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

65083107-65110160 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 65090830 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Methionine at position 165 (I165M)

Ref Sequence

ENSEMBL: ENSMUSP00000112953 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000120580] [ENSMUST00000129956] [ENSMUST00000223315] [ENSMUST00000223341]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000120580
AA Change: I165M

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000112953
Gene: ENSMUSG00000035597
AA Change: I165M

Domain	Start	End	E-Value	Type
HAT	107	139	3.71e-2	SMART
HAT	141	173	4.39e-4	SMART
HAT	181	216	2.07e0	SMART
HAT	218	251	1.36e2	SMART
low complexity region	277	290	N/A	INTRINSIC
Blast:HAT	323	363	6e-18	BLAST
HAT	365	397	3.2e-6	SMART
HAT	398	431	3.21e1	SMART
HAT	505	537	3.63e1	SMART
low complexity region	645	664	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000129956

SMART Domains

Protein: ENSMUSP00000114713
Gene: ENSMUSG00000035597

Domain	Start	End	E-Value	Type
Blast:HAT	107	139	7e-17	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000220462

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000220798

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000221221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000222154

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000223105

Predicted Effect

possibly damaging
Transcript: ENSMUST00000223315
AA Change: I46M

PolyPhen 2 Score 0.801 (Sensitivity: 0.84; Specificity: 0.93)

Predicted Effect

probably benign
Transcript: ENSMUST00000223341

Meta Mutation Damage Score

0.0840

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.9%
20x: 91.3%

Validation Efficiency

99% (87/88)

Allele List at MGI

Other mutations in this stock

Total: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700102P08Rik	A	T	9: 108,272,498 (GRCm39)	D136V	probably damaging	Het
Ankrd17	G	A	5: 90,447,891 (GRCm39)	R217W	probably damaging	Het
Ankrd23	A	T	1: 36,571,068 (GRCm39)	H102Q	probably damaging	Het
Arfip2	G	T	7: 105,287,151 (GRCm39)	R138S	probably damaging	Het
Arhgap27	A	T	11: 103,229,949 (GRCm39)		probably null	Het
Atg2a	T	C	19: 6,307,563 (GRCm39)	L1499P	probably damaging	Het
Bnc2	A	G	4: 84,194,416 (GRCm39)	S110P	probably damaging	Het
Ccdc171	T	C	4: 83,476,829 (GRCm39)		probably benign	Het
Ccdc7a	A	G	8: 129,706,535 (GRCm39)		probably benign	Het
Chd5	T	C	4: 152,467,768 (GRCm39)	S1689P	probably benign	Het
Corin	A	G	5: 72,529,525 (GRCm39)	C212R	probably damaging	Het
Cyp2c65	A	G	19: 39,049,597 (GRCm39)	I42V	probably benign	Het
Cyp3a25	G	A	5: 145,928,266 (GRCm39)	R260C	probably damaging	Het
Dock6	T	C	9: 21,757,087 (GRCm39)	Y116C	probably damaging	Het
Eif3a	A	G	19: 60,751,656 (GRCm39)		probably benign	Het
Epop	T	C	11: 97,519,143 (GRCm39)	D322G	probably damaging	Het
Eps8l3	T	A	3: 107,798,004 (GRCm39)		probably benign	Het
Exph5	T	C	9: 53,287,925 (GRCm39)	S1669P	possibly damaging	Het
Faah	A	T	4: 115,856,823 (GRCm39)		probably benign	Het
Fanca	A	G	8: 124,030,724 (GRCm39)	C453R	probably benign	Het
Fcgbp	T	A	7: 27,785,660 (GRCm39)	C366S	probably damaging	Het
Fmn2	A	G	1: 174,329,981 (GRCm39)	T124A	unknown	Het
Foxi3	C	T	6: 70,933,996 (GRCm39)	S161L	probably damaging	Het
Foxo3	A	T	10: 42,073,020 (GRCm39)	V499E	probably damaging	Het
Gas2l3	CACTCGTCATACT	CACT	10: 89,266,820 (GRCm39)		probably benign	Het
Gbgt1	T	C	2: 28,393,182 (GRCm39)	V90A	probably damaging	Het
Gm839	A	C	6: 89,189,581 (GRCm39)		noncoding transcript	Het
Gtf3c2	T	C	5: 31,326,467 (GRCm39)	E348G	possibly damaging	Het
Hnrnpm	G	T	17: 33,868,775 (GRCm39)	R551S	probably damaging	Het
Hspa1l	A	G	17: 35,197,199 (GRCm39)	T413A	possibly damaging	Het
Hspg2	T	C	4: 137,269,841 (GRCm39)	Y2297H	probably damaging	Het
Ighv1-81	T	A	12: 115,884,093 (GRCm39)	I53L	probably benign	Het
Kcnj11	C	T	7: 45,748,544 (GRCm39)	V260I	probably benign	Het
Krt84	A	G	15: 101,438,689 (GRCm39)	V266A	probably benign	Het
Lgals3bp	T	C	11: 118,284,781 (GRCm39)	Y266C	probably damaging	Het
Lrrc41	T	C	4: 115,946,521 (GRCm39)	V412A	possibly damaging	Het
Map4k4	A	T	1: 40,056,385 (GRCm39)	E1023D	probably damaging	Het
Mark3	T	A	12: 111,584,758 (GRCm39)	L118*	probably null	Het
Mrgpra9	T	A	7: 46,884,759 (GRCm39)	T303S	possibly damaging	Het
Mterf4	T	C	1: 93,232,647 (GRCm39)	E68G	probably benign	Het
Nckap5	A	C	1: 126,456,378 (GRCm39)		probably benign	Het
Nox3	T	A	17: 3,720,169 (GRCm39)	T339S	probably damaging	Het
Nrip2	A	C	6: 128,385,337 (GRCm39)	H256P	probably benign	Het
Oas1d	T	C	5: 121,053,831 (GRCm39)	V97A	probably benign	Het
Obox2	T	A	7: 15,131,102 (GRCm39)		probably null	Het
Opa1	T	C	16: 29,467,791 (GRCm39)	F989S	possibly damaging	Het
Or10g9	T	C	9: 39,912,319 (GRCm39)		probably null	Het
Padi1	T	A	4: 140,552,158 (GRCm39)	I429F	probably damaging	Het
Paics	A	G	5: 77,109,051 (GRCm39)	D163G	probably damaging	Het
Pik3c2b	G	T	1: 133,027,364 (GRCm39)	E1288*	probably null	Het
Prdm16	A	T	4: 154,426,009 (GRCm39)	V593D	possibly damaging	Het
Pth2r	A	G	1: 65,361,143 (GRCm39)	T26A	probably benign	Het
Ptpn21	T	C	12: 98,681,454 (GRCm39)		probably null	Het
Rab44	C	T	17: 29,358,529 (GRCm39)	A239V	probably benign	Het
Rtcb	T	C	10: 85,791,600 (GRCm39)	N52S	probably benign	Het
Sapcd2	T	A	2: 25,263,578 (GRCm39)		probably null	Het
Scaf11	T	C	15: 96,316,123 (GRCm39)	E1147G	possibly damaging	Het
Selenoo	T	C	15: 88,983,881 (GRCm39)	Y595H	probably damaging	Het
Slc2a5	G	T	4: 150,205,199 (GRCm39)	E3*	probably null	Het
Snw1	A	G	12: 87,499,428 (GRCm39)	V391A	probably benign	Het
Sorbs2	A	G	8: 46,249,254 (GRCm39)	K755R	probably benign	Het
Sorbs3	G	T	14: 70,424,394 (GRCm39)	P513T	probably damaging	Het
Sowaha	T	A	11: 53,370,337 (GRCm39)	E133V	possibly damaging	Het
Srsf5	T	C	12: 80,994,075 (GRCm39)		probably benign	Het
St8sia5	T	A	18: 77,342,478 (GRCm39)	M396K	possibly damaging	Het
Tcp11l1	T	C	2: 104,512,130 (GRCm39)	I501V	probably benign	Het
Tert	A	G	13: 73,796,508 (GRCm39)	K1080E	possibly damaging	Het
Tescl	T	A	7: 24,033,323 (GRCm39)	M1L	possibly damaging	Het
Thop1	T	A	10: 80,909,201 (GRCm39)		probably null	Het
Tmtc4	T	C	14: 123,210,618 (GRCm39)	H80R	probably damaging	Het
Toe1	C	T	4: 116,661,729 (GRCm39)	S480N	probably damaging	Het
Trap1	C	A	16: 3,863,352 (GRCm39)	V557F	probably benign	Het
Trim30d	T	C	7: 104,132,564 (GRCm39)	E91G	probably benign	Het
Ttf1	C	T	2: 28,954,668 (GRCm39)	H11Y	possibly damaging	Het
Ttll8	C	A	15: 88,798,368 (GRCm39)	G789V	probably damaging	Het
Ulk4	A	G	9: 121,087,798 (GRCm39)	F298S	probably benign	Het
Wwc1	C	T	11: 35,780,227 (GRCm39)	A243T	probably benign	Het
Zfp248	A	C	6: 118,406,787 (GRCm39)	H267Q	possibly damaging	Het
Zfyve26	T	A	12: 79,321,785 (GRCm39)	M945L	probably benign	Het
Zup1	T	C	10: 33,825,434 (GRCm39)	D16G	probably damaging	Het

Other mutations in Prpf39

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00834:Prpf39	APN	12	65,090,037 (GRCm39)	missense	probably damaging	0.99
IGL01025:Prpf39	APN	12	65,089,255 (GRCm39)	unclassified	probably benign
IGL01323:Prpf39	APN	12	65,089,498 (GRCm39)	missense	possibly damaging	0.70
IGL02346:Prpf39	APN	12	65,104,510 (GRCm39)	missense	probably benign	0.02
IGL02966:Prpf39	APN	12	65,089,553 (GRCm39)	missense	probably benign	0.45
IGL03189:Prpf39	APN	12	65,090,076 (GRCm39)	nonsense	probably null
IGL03357:Prpf39	APN	12	65,108,211 (GRCm39)	unclassified	probably benign
R0103:Prpf39	UTSW	12	65,102,057 (GRCm39)	missense	possibly damaging	0.56
R0103:Prpf39	UTSW	12	65,102,057 (GRCm39)	missense	possibly damaging	0.56
R0328:Prpf39	UTSW	12	65,090,145 (GRCm39)	splice site	probably benign
R0549:Prpf39	UTSW	12	65,103,030 (GRCm39)	missense	probably benign	0.05
R0840:Prpf39	UTSW	12	65,094,980 (GRCm39)	missense	probably benign	0.21
R1248:Prpf39	UTSW	12	65,100,740 (GRCm39)	splice site	probably benign
R1322:Prpf39	UTSW	12	65,089,436 (GRCm39)	missense	possibly damaging	0.48
R1481:Prpf39	UTSW	12	65,100,088 (GRCm39)	missense	probably damaging	1.00
R2209:Prpf39	UTSW	12	65,104,689 (GRCm39)	critical splice donor site	probably null
R2232:Prpf39	UTSW	12	65,090,786 (GRCm39)	nonsense	probably null
R2507:Prpf39	UTSW	12	65,104,589 (GRCm39)	missense	probably benign	0.36
R2508:Prpf39	UTSW	12	65,104,589 (GRCm39)	missense	probably benign	0.36
R2959:Prpf39	UTSW	12	65,089,297 (GRCm39)	missense	probably damaging	1.00
R3117:Prpf39	UTSW	12	65,104,651 (GRCm39)	missense	possibly damaging	0.79
R3118:Prpf39	UTSW	12	65,104,651 (GRCm39)	missense	possibly damaging	0.79
R3980:Prpf39	UTSW	12	65,108,231 (GRCm39)	unclassified	probably benign
R4407:Prpf39	UTSW	12	65,103,040 (GRCm39)	missense	probably damaging	1.00
R4620:Prpf39	UTSW	12	65,089,337 (GRCm39)	missense	probably benign
R5154:Prpf39	UTSW	12	65,095,051 (GRCm39)	missense	probably benign	0.29
R6248:Prpf39	UTSW	12	65,089,528 (GRCm39)	missense	probably damaging	1.00
R6334:Prpf39	UTSW	12	65,089,587 (GRCm39)	splice site	probably null
R6614:Prpf39	UTSW	12	65,089,337 (GRCm39)	missense	probably benign
R6749:Prpf39	UTSW	12	65,103,048 (GRCm39)	missense	possibly damaging	0.94
R6944:Prpf39	UTSW	12	65,089,454 (GRCm39)	missense	probably benign	0.03
R7023:Prpf39	UTSW	12	65,100,074 (GRCm39)	missense	possibly damaging	0.94
R7503:Prpf39	UTSW	12	65,100,167 (GRCm39)	missense	probably benign	0.04
R7532:Prpf39	UTSW	12	65,100,145 (GRCm39)	missense	probably benign	0.00
R7608:Prpf39	UTSW	12	65,100,220 (GRCm39)	missense	probably benign	0.41
R8286:Prpf39	UTSW	12	65,103,132 (GRCm39)	missense	probably benign
R8439:Prpf39	UTSW	12	65,102,036 (GRCm39)	missense	possibly damaging	0.95
R8787:Prpf39	UTSW	12	65,089,555 (GRCm39)	missense	possibly damaging	0.95
R9101:Prpf39	UTSW	12	65,090,078 (GRCm39)	missense	probably damaging	1.00
R9153:Prpf39	UTSW	12	65,106,671 (GRCm39)	missense	probably damaging	0.99
R9448:Prpf39	UTSW	12	65,108,034 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GTGGGGATCAGAACATTGCC -3'
(R):5'- GACTGCATGTCTTAAGTAATCACAC -3'

Sequencing Primer
(F):5'- ACATTGCCATGTTCTATCCAAC -3'
(R):5'- CCAGTTTAGCATTCACAAAT -3'

Posted On

2016-04-15