Mutagenetix > Incidental Mutation

Incidental Mutation 'R1837:Rpap1'

205370

Institutional Source

Beutler Lab

Gene Symbol

Rpap1

Ensembl Gene

ENSMUSG00000034032

Gene Name

RNA polymerase II associated protein 1

Synonyms

A730023M06Rik, 1190005L06Rik

MMRRC Submission

039864-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.966) question?

Stock #

R1837 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

119594440-119618018 bp(-) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

A to C at 119600366 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000106420 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000048493] [ENSMUST00000099529] [ENSMUST00000110793] [ENSMUST00000110793] [ENSMUST00000136419] [ENSMUST00000184294]

AlphaFold

Q80TE0

Predicted Effect

probably null
Transcript: ENSMUST00000048493

SMART Domains

Protein: ENSMUSP00000037275
Gene: ENSMUSG00000034032

Domain	Start	End	E-Value	Type
low complexity region	62	81	N/A	INTRINSIC
Pfam:RPAP1_N	225	270	2.4e-21	PFAM
Pfam:RPAP1_C	372	438	1.9e-27	PFAM
low complexity region	451	473	N/A	INTRINSIC
low complexity region	476	488	N/A	INTRINSIC
low complexity region	515	529	N/A	INTRINSIC
low complexity region	739	752	N/A	INTRINSIC
low complexity region	843	860	N/A	INTRINSIC
low complexity region	989	1007	N/A	INTRINSIC
low complexity region	1042	1052	N/A	INTRINSIC
low complexity region	1097	1108	N/A	INTRINSIC
low complexity region	1193	1204	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000099529

SMART Domains

Protein: ENSMUSP00000097127
Gene: ENSMUSG00000034032

Domain	Start	End	E-Value	Type
low complexity region	62	81	N/A	INTRINSIC
Pfam:RPAP1_N	224	272	1.7e-21	PFAM
Pfam:RPAP1_C	370	440	2.9e-27	PFAM
low complexity region	451	473	N/A	INTRINSIC
low complexity region	476	488	N/A	INTRINSIC
low complexity region	515	529	N/A	INTRINSIC
low complexity region	739	752	N/A	INTRINSIC
low complexity region	843	860	N/A	INTRINSIC
low complexity region	989	1007	N/A	INTRINSIC
low complexity region	1042	1052	N/A	INTRINSIC
low complexity region	1097	1108	N/A	INTRINSIC
low complexity region	1193	1204	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000110793

SMART Domains

Protein: ENSMUSP00000106420
Gene: ENSMUSG00000034032

Domain	Start	End	E-Value	Type
low complexity region	62	81	N/A	INTRINSIC
Pfam:RPAP1_N	224	272	1.7e-21	PFAM
Pfam:RPAP1_C	370	440	2.9e-27	PFAM
low complexity region	451	473	N/A	INTRINSIC
low complexity region	476	488	N/A	INTRINSIC
low complexity region	515	529	N/A	INTRINSIC
low complexity region	739	752	N/A	INTRINSIC
low complexity region	843	860	N/A	INTRINSIC
low complexity region	989	1007	N/A	INTRINSIC
low complexity region	1042	1052	N/A	INTRINSIC
low complexity region	1097	1108	N/A	INTRINSIC
low complexity region	1193	1204	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000110793

SMART Domains

Protein: ENSMUSP00000106420
Gene: ENSMUSG00000034032

Domain	Start	End	E-Value	Type
low complexity region	62	81	N/A	INTRINSIC
Pfam:RPAP1_N	224	272	1.7e-21	PFAM
Pfam:RPAP1_C	370	440	2.9e-27	PFAM
low complexity region	451	473	N/A	INTRINSIC
low complexity region	476	488	N/A	INTRINSIC
low complexity region	515	529	N/A	INTRINSIC
low complexity region	739	752	N/A	INTRINSIC
low complexity region	843	860	N/A	INTRINSIC
low complexity region	989	1007	N/A	INTRINSIC
low complexity region	1042	1052	N/A	INTRINSIC
low complexity region	1097	1108	N/A	INTRINSIC
low complexity region	1193	1204	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000136419

SMART Domains

Protein: ENSMUSP00000138619
Gene: ENSMUSG00000034032

Domain	Start	End	E-Value	Type
low complexity region	62	81	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139311

Predicted Effect

probably benign
Transcript: ENSMUST00000184294

SMART Domains

Protein: ENSMUSP00000138873
Gene: ENSMUSG00000034032

Domain	Start	End	E-Value	Type
low complexity region	62	81	N/A	INTRINSIC
Pfam:RPAP1_N	224	272	4.8e-22	PFAM
Pfam:RPAP1_C	370	440	1.2e-27	PFAM
low complexity region	451	473	N/A	INTRINSIC
low complexity region	476	488	N/A	INTRINSIC
low complexity region	515	529	N/A	INTRINSIC
low complexity region	739	752	N/A	INTRINSIC
low complexity region	843	860	N/A	INTRINSIC

Meta Mutation Damage Score

0.9494

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 94.9%
20x: 91.6%

Validation Efficiency

99% (86/87)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This protein forms part of the RNA polymerase II (RNAPII) enzyme complex and may recruit RNAPII to chromatin through its interaction with acetylated histones. [provided by RefSeq, Jul 2012]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actl10	G	T	2: 154,394,962 (GRCm39)	G305W	probably damaging	Het
Actr3b	A	T	5: 26,030,157 (GRCm39)	T74S	probably benign	Het
Add2	A	G	6: 86,095,540 (GRCm39)	E652G	probably damaging	Het
Alg9	T	A	9: 50,717,615 (GRCm39)	V83D	probably damaging	Het
Atp13a2	T	A	4: 140,721,643 (GRCm39)	Y244*	probably null	Het
BB014433	C	G	8: 15,092,629 (GRCm39)	V75L	unknown	Het
Bcr	A	G	10: 75,003,932 (GRCm39)		probably benign	Het
Begain	G	A	12: 109,001,249 (GRCm39)		probably benign	Het
Bzw1	A	G	1: 58,439,277 (GRCm39)	K67E	probably damaging	Het
Ccdc141	T	C	2: 76,842,009 (GRCm39)	E1474G	probably benign	Het
Cdc73	T	A	1: 143,543,395 (GRCm39)	T314S	possibly damaging	Het
Cfap206	T	C	4: 34,728,813 (GRCm39)	T31A	probably damaging	Het
Cfap58	G	A	19: 48,017,578 (GRCm39)	E813K	probably damaging	Het
Clstn2	C	A	9: 97,465,593 (GRCm39)	A133S	probably benign	Het
Col14a1	A	T	15: 55,245,891 (GRCm39)	D465V	unknown	Het
Col2a1	C	T	15: 97,894,522 (GRCm39)		probably benign	Het
Dab2	A	G	15: 6,365,957 (GRCm39)		probably benign	Het
Eme1	T	C	11: 94,536,787 (GRCm39)	D464G	probably benign	Het
Eml6	T	C	11: 29,699,802 (GRCm39)		probably null	Het
Ern1	C	A	11: 106,349,783 (GRCm39)	L44F	probably damaging	Het
Fam111a	T	A	19: 12,564,816 (GRCm39)	S188R	probably benign	Het
Fam151b	A	T	13: 92,610,639 (GRCm39)		probably benign	Het
Fmo6	T	C	1: 162,750,379 (GRCm39)	N226D	probably benign	Het
Ggt1	A	G	10: 75,415,128 (GRCm39)	D214G	probably benign	Het
Gm14226	A	G	2: 154,866,930 (GRCm39)	I296V	probably benign	Het
Gm9915	A	T	1: 42,269,847 (GRCm39)		noncoding transcript	Het
Heatr5b	T	C	17: 79,128,180 (GRCm39)	D485G	possibly damaging	Het
Helz2	A	T	2: 180,871,082 (GRCm39)	I2785N	probably damaging	Het
Htt	C	T	5: 34,976,367 (GRCm39)	T723M	probably benign	Het
Hydin	C	A	8: 111,296,257 (GRCm39)	H3595Q	probably benign	Het
Il6ra	T	C	3: 89,797,579 (GRCm39)	D96G	probably benign	Het
Kif5a	G	A	10: 127,072,684 (GRCm39)	Q702*	probably null	Het
Klhdc7a	G	T	4: 139,694,381 (GRCm39)	P189T	probably benign	Het
Krt7	A	G	15: 101,317,463 (GRCm39)	D252G	probably benign	Het
Lad1	C	A	1: 135,757,444 (GRCm39)	D394E	probably benign	Het
Lhx8	A	T	3: 154,033,692 (GRCm39)	C38S	possibly damaging	Het
Lta4h	C	T	10: 93,305,037 (GRCm39)	T280M	probably damaging	Het
Magi2	A	T	5: 20,670,825 (GRCm39)	T163S	probably damaging	Het
Med1	G	T	11: 98,060,238 (GRCm39)	D230E	probably damaging	Het
Mmp1b	A	T	9: 7,386,409 (GRCm39)	F171I	probably damaging	Het
Mprip	T	C	11: 59,657,571 (GRCm39)	V801A	probably damaging	Het
Mtrf1	A	G	14: 79,639,273 (GRCm39)	E135G	possibly damaging	Het
Muc5ac	T	A	7: 141,360,823 (GRCm39)	M1378K	probably benign	Het
Myo3a	A	T	2: 22,467,604 (GRCm39)	Q286L	possibly damaging	Het
Ndor1	C	T	2: 25,138,408 (GRCm39)	G391R	probably damaging	Het
Nefl	C	T	14: 68,324,075 (GRCm39)	R438C	probably damaging	Het
Nlrp3	G	A	11: 59,439,742 (GRCm39)	V440I	probably benign	Het
Notch3	A	T	17: 32,343,296 (GRCm39)	L1959Q	probably damaging	Het
Noto	A	G	6: 85,401,159 (GRCm39)	T63A	probably benign	Het
Oc90	G	A	15: 65,761,529 (GRCm39)	T163M	probably damaging	Het
Or1l4	T	A	2: 37,092,114 (GRCm39)	M287K	probably benign	Het
Or4c114	A	T	2: 88,905,176 (GRCm39)	Y86*	probably null	Het
Or5an10	A	G	19: 12,275,740 (GRCm39)	V252A	probably damaging	Het
Pdpr	C	A	8: 111,861,366 (GRCm39)	P787T	probably damaging	Het
Phlda1	A	G	10: 111,343,092 (GRCm39)	Q276R	probably benign	Het
Ptpn21	T	G	12: 98,699,885 (GRCm39)	K10Q	probably damaging	Het
Ptprb	A	G	10: 116,177,531 (GRCm39)	E1364G	probably benign	Het
Rabep1	T	A	11: 70,795,484 (GRCm39)	W237R	probably damaging	Het
Rai1	A	T	11: 60,080,224 (GRCm39)	K1429N	probably damaging	Het
Rapgef1	A	G	2: 29,627,438 (GRCm39)	I1027M	probably damaging	Het
Rit1	C	G	3: 88,636,477 (GRCm39)	T127S	probably damaging	Het
Senp7	T	A	16: 55,978,879 (GRCm39)	C471S	probably benign	Het
Slc16a14	A	G	1: 84,890,120 (GRCm39)	V395A	probably benign	Het
Slc45a1	C	T	4: 150,722,916 (GRCm39)	G323S	probably benign	Het
Syne2	A	T	12: 76,014,434 (GRCm39)	E3208D	probably damaging	Het
Tap1	C	T	17: 34,407,083 (GRCm39)	A77V	possibly damaging	Het
Ticam1	T	C	17: 56,577,799 (GRCm39)	E432G	possibly damaging	Het
Tmem192	C	A	8: 65,416,992 (GRCm39)		probably benign	Het
Trub1	T	C	19: 57,441,461 (GRCm39)	V28A	probably benign	Het
Ttc21b	A	T	2: 66,028,106 (GRCm39)	L1121H	probably benign	Het
Ttc38	A	G	15: 85,735,764 (GRCm39)	D290G	probably damaging	Het
Ulk1	C	T	5: 110,937,247 (GRCm39)	G683D	probably damaging	Het
Vmn1r122	A	T	7: 20,867,291 (GRCm39)	F255I	probably benign	Het
Vmn2r68	T	A	7: 84,882,886 (GRCm39)	I289F	probably damaging	Het
Vps39	A	T	2: 120,155,878 (GRCm39)	L514H	probably damaging	Het
Wdr48	T	G	9: 119,734,482 (GRCm39)	S134A	probably damaging	Het
Yap1	A	T	9: 7,962,350 (GRCm39)	Y139N	probably damaging	Het
Ylpm1	T	C	12: 85,076,107 (GRCm39)	V486A	possibly damaging	Het
Zbtb38	T	C	9: 96,569,048 (GRCm39)	T679A	probably benign	Het
Zfp292	A	G	4: 34,810,264 (GRCm39)	S927P	probably damaging	Het
Zfp324	C	T	7: 12,704,156 (GRCm39)	T115I	probably benign	Het
Zfp523	T	A	17: 28,413,967 (GRCm39)	I34N	probably damaging	Het
Zfp945	A	T	17: 23,070,247 (GRCm39)	C551S	probably damaging	Het
Zfp958	A	G	8: 4,678,590 (GRCm39)	H205R	probably damaging	Het
Zfp974	G	A	7: 27,609,781 (GRCm39)	P648L	possibly damaging	Het

Other mutations in Rpap1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01807:Rpap1	APN	2	119,613,189 (GRCm39)	missense	possibly damaging	0.50
IGL02009:Rpap1	APN	2	119,610,594 (GRCm39)	missense	possibly damaging	0.51
IGL02068:Rpap1	APN	2	119,613,135 (GRCm39)	missense	probably benign	0.02
IGL02100:Rpap1	APN	2	119,599,807 (GRCm39)	missense	probably benign	0.06
IGL02528:Rpap1	APN	2	119,605,431 (GRCm39)	splice site	probably null
IGL02530:Rpap1	APN	2	119,613,720 (GRCm39)	splice site	probably benign
IGL02747:Rpap1	APN	2	119,604,609 (GRCm39)	missense	probably damaging	0.98
IGL03371:Rpap1	APN	2	119,605,538 (GRCm39)	splice site	probably benign
R0138:Rpap1	UTSW	2	119,595,380 (GRCm39)	splice site	probably null
R0325:Rpap1	UTSW	2	119,602,321 (GRCm39)	missense	probably benign
R0616:Rpap1	UTSW	2	119,608,601 (GRCm39)	missense	probably damaging	1.00
R1081:Rpap1	UTSW	2	119,601,750 (GRCm39)	missense	probably damaging	1.00
R1657:Rpap1	UTSW	2	119,614,259 (GRCm39)	missense	possibly damaging	0.53
R2307:Rpap1	UTSW	2	119,614,247 (GRCm39)	missense	probably benign	0.00
R2308:Rpap1	UTSW	2	119,614,247 (GRCm39)	missense	probably benign	0.00
R2375:Rpap1	UTSW	2	119,600,888 (GRCm39)	missense	possibly damaging	0.50
R2507:Rpap1	UTSW	2	119,610,535 (GRCm39)	critical splice donor site	probably null
R2508:Rpap1	UTSW	2	119,610,535 (GRCm39)	critical splice donor site	probably null
R4155:Rpap1	UTSW	2	119,604,660 (GRCm39)	missense	probably damaging	1.00
R4156:Rpap1	UTSW	2	119,604,660 (GRCm39)	missense	probably damaging	1.00
R4157:Rpap1	UTSW	2	119,604,660 (GRCm39)	missense	probably damaging	1.00
R4657:Rpap1	UTSW	2	119,605,487 (GRCm39)	missense	probably benign	0.03
R4837:Rpap1	UTSW	2	119,608,732 (GRCm39)	missense	probably benign	0.32
R4880:Rpap1	UTSW	2	119,614,346 (GRCm39)	missense	probably damaging	0.97
R5010:Rpap1	UTSW	2	119,600,522 (GRCm39)	missense	probably benign
R5111:Rpap1	UTSW	2	119,601,728 (GRCm39)	missense	probably damaging	1.00
R5650:Rpap1	UTSW	2	119,604,331 (GRCm39)	missense	probably benign
R6144:Rpap1	UTSW	2	119,603,128 (GRCm39)	nonsense	probably null
R6353:Rpap1	UTSW	2	119,607,377 (GRCm39)	splice site	probably null
R6646:Rpap1	UTSW	2	119,610,612 (GRCm39)	missense	probably benign	0.03
R6731:Rpap1	UTSW	2	119,608,777 (GRCm39)	missense	probably benign
R6872:Rpap1	UTSW	2	119,605,850 (GRCm39)	missense	probably damaging	1.00
R6878:Rpap1	UTSW	2	119,608,657 (GRCm39)	missense	probably damaging	1.00
R7060:Rpap1	UTSW	2	119,604,043 (GRCm39)	missense	probably damaging	1.00
R7558:Rpap1	UTSW	2	119,601,735 (GRCm39)	missense	probably benign
R7640:Rpap1	UTSW	2	119,594,891 (GRCm39)	missense	possibly damaging	0.63
R7862:Rpap1	UTSW	2	119,605,893 (GRCm39)	critical splice acceptor site	probably null
R8055:Rpap1	UTSW	2	119,595,284 (GRCm39)	missense	probably benign	0.13
R8934:Rpap1	UTSW	2	119,599,730 (GRCm39)	critical splice donor site	probably null
R9032:Rpap1	UTSW	2	119,608,776 (GRCm39)	missense	probably benign	0.00
R9220:Rpap1	UTSW	2	119,604,669 (GRCm39)	missense	probably damaging	0.99
R9422:Rpap1	UTSW	2	119,613,519 (GRCm39)	intron	probably benign
R9651:Rpap1	UTSW	2	119,598,484 (GRCm39)	missense	probably damaging	1.00
R9776:Rpap1	UTSW	2	119,607,278 (GRCm39)	missense	probably benign	0.00
X0028:Rpap1	UTSW	2	119,601,543 (GRCm39)	missense	probably benign
Z1177:Rpap1	UTSW	2	119,614,233 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GAAAGTAGTTCTGGAGTCCTGG -3'
(R):5'- ATGTCTGTTCTCCCTGCAGG -3'

Sequencing Primer
(F):5'- TCCTGGGGCAGTCAACACAG -3'
(R):5'- TGCAATCCGCTGTCCTGTG -3'

Posted On

2014-06-23