Mutagenetix > Incidental Mutation

Incidental Mutation 'R0138:Rpap1'

22086

Institutional Source

Beutler Lab

Gene Symbol

Rpap1

Ensembl Gene

ENSMUSG00000034032

Gene Name

RNA polymerase II associated protein 1

Synonyms

A730023M06Rik, 1190005L06Rik

MMRRC Submission

038423-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.965) question?

Stock #

R0138 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

119594440-119618018 bp(-) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to C at 119595380 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000080774 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028759] [ENSMUST00000048493] [ENSMUST00000082130] [ENSMUST00000099529] [ENSMUST00000110793] [ENSMUST00000136419] [ENSMUST00000184294]

AlphaFold

Q80TE0

Predicted Effect

probably null
Transcript: ENSMUST00000028759

SMART Domains

Protein: ENSMUSP00000028759
Gene: ENSMUSG00000027297

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
Pfam:Gly_rich	111	381	2.4e-21	PFAM
transmembrane domain	423	445	N/A	INTRINSIC
TyrKc	506	773	2.61e-127	SMART
low complexity region	824	841	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000048493
AA Change: E1287G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000037275
Gene: ENSMUSG00000034032
AA Change: E1287G

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: ENSMUST00000082130

SMART Domains

Protein: ENSMUSP00000080774
Gene: ENSMUSG00000027297

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
Pfam:Gly_rich	109	294	6.1e-16	PFAM
transmembrane domain	362	384	N/A	INTRINSIC
TyrKc	445	712	2.61e-127	SMART
low complexity region	763	780	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000099529
AA Change: E1287G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000097127
Gene: ENSMUSG00000034032
AA Change: E1287G

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 damaging
Transcript: ENSMUST00000110793
AA Change: E1287G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000106420
Gene: ENSMUSG00000034032
AA Change: E1287G

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

0.9673

Coding Region Coverage

1x: 99.0%
3x: 98.3%
10x: 96.4%
20x: 92.8%

Validation Efficiency

97% (76/78)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca4	T	A	3: 121,899,098 (GRCm39)	N693K	probably damaging	Het
Adgrl3	T	A	5: 81,841,454 (GRCm39)	V845D	probably damaging	Het
Anxa8	T	A	14: 33,819,896 (GRCm39)	F269Y	probably benign	Het
Anxa8	T	A	14: 33,819,897 (GRCm39)	F295L	possibly damaging	Het
Aox4	C	G	1: 58,268,025 (GRCm39)	L202V	probably damaging	Het
Ap3s2	A	G	7: 79,559,617 (GRCm39)	V104A	probably benign	Het
Aqp3	G	A	4: 41,094,843 (GRCm39)		probably benign	Het
Arhgef26	C	T	3: 62,355,680 (GRCm39)	H751Y	probably benign	Het
Asic4	A	T	1: 75,446,331 (GRCm39)	Q291L	possibly damaging	Het
Bap1	T	C	14: 30,978,681 (GRCm39)	Y31H	probably damaging	Het
Brf1	A	T	12: 112,924,759 (GRCm39)	V655D	probably damaging	Het
Cebpz	A	G	17: 79,238,820 (GRCm39)	S663P	probably benign	Het
Ces2h	A	G	8: 105,744,693 (GRCm39)	D357G	probably benign	Het
Cfap36	T	C	11: 29,194,073 (GRCm39)	T90A	probably benign	Het
Ciita	A	T	16: 10,330,134 (GRCm39)	D803V	probably damaging	Het
Clnk	C	A	5: 38,931,951 (GRCm39)		probably benign	Het
Cyp46a1	A	G	12: 108,317,470 (GRCm39)	N158S	probably damaging	Het
Cyp4f13	A	G	17: 33,160,080 (GRCm39)	I98T	possibly damaging	Het
Def8	G	A	8: 124,183,234 (GRCm39)	A278T	probably damaging	Het
Dll3	T	A	7: 28,000,746 (GRCm39)	D103V	possibly damaging	Het
Dnai1	T	A	4: 41,629,814 (GRCm39)	M446K	possibly damaging	Het
Dppa4	A	T	16: 48,111,425 (GRCm39)	T85S	probably benign	Het
Eif4g1	A	T	16: 20,494,095 (GRCm39)	H57L	probably damaging	Het
Fmnl3	G	C	15: 99,220,619 (GRCm39)		probably benign	Het
Fn1	T	A	1: 71,663,269 (GRCm39)	Q1073L	possibly damaging	Het
Foxp4	T	C	17: 48,180,104 (GRCm39)	D599G	unknown	Het
Frrs1	T	C	3: 116,675,456 (GRCm39)	V128A	possibly damaging	Het
Gcfc2	G	A	6: 81,926,935 (GRCm39)	D608N	probably damaging	Het
Gm1043	T	C	5: 37,350,317 (GRCm39)		probably benign	Het
Gm5148	T	C	3: 37,768,926 (GRCm39)	E98G	probably benign	Het
Gpr141	T	C	13: 19,936,428 (GRCm39)	I116V	probably benign	Het
Hic1	T	C	11: 75,058,169 (GRCm39)	N240S	probably damaging	Het
Hpx	G	A	7: 105,241,445 (GRCm39)	T322I	probably damaging	Het
Hs3st4	A	T	7: 123,996,416 (GRCm39)	M361L	probably benign	Het
Ifrd1	A	G	12: 40,257,129 (GRCm39)		probably benign	Het
Ino80	G	A	2: 119,213,441 (GRCm39)	R1249C	probably damaging	Het
Klk1b21	T	A	7: 43,755,319 (GRCm39)	C173S	probably damaging	Het
Krt25	A	T	11: 99,213,524 (GRCm39)	V65E	probably benign	Het
Lrrc15	A	T	16: 30,092,267 (GRCm39)	D357E	possibly damaging	Het
Lrrd1	T	A	5: 3,901,345 (GRCm39)	V550E	probably benign	Het
Macf1	A	G	4: 123,334,540 (GRCm39)	Y1490H	probably damaging	Het
Macrod1	A	G	19: 7,174,281 (GRCm39)		probably benign	Het
Mcm5	T	A	8: 75,847,508 (GRCm39)	V435D	probably damaging	Het
Mctp1	C	T	13: 76,975,831 (GRCm39)	R478C	probably damaging	Het
Med10	T	C	13: 69,959,817 (GRCm39)		probably benign	Het
Mrpl4	T	C	9: 20,919,888 (GRCm39)	Y280H	probably benign	Het
Msrb3	T	C	10: 120,687,892 (GRCm39)	E61G	probably damaging	Het
Myo1c	T	C	11: 75,551,827 (GRCm39)	Y337H	possibly damaging	Het
Myo7b	T	A	18: 32,143,204 (GRCm39)	T165S	probably damaging	Het
Myrfl	T	A	10: 116,685,138 (GRCm39)	R81W	probably damaging	Het
Neil1	T	C	9: 57,051,030 (GRCm39)		probably benign	Het
Neto2	A	G	8: 86,367,673 (GRCm39)	I357T	possibly damaging	Het
Nfat5	C	T	8: 108,065,707 (GRCm39)	R156W	probably damaging	Het
Nkx6-3	T	C	8: 23,643,607 (GRCm39)	S3P	probably benign	Het
Or52h7	A	T	7: 104,214,210 (GRCm39)	I261L	probably benign	Het
Plce1	T	C	19: 38,512,863 (GRCm39)	I54T	possibly damaging	Het
Prex2	A	T	1: 11,355,267 (GRCm39)		probably benign	Het
Psapl1	T	A	5: 36,361,975 (GRCm39)	V189E	probably damaging	Het
Ptdss2	T	G	7: 140,735,232 (GRCm39)		probably benign	Het
Rnf213	T	C	11: 119,307,322 (GRCm39)	C661R	probably benign	Het
Rrp1b	A	G	17: 32,279,426 (GRCm39)	T696A	probably benign	Het
Sacm1l	T	A	9: 123,377,982 (GRCm39)	H87Q	probably benign	Het
Serpinb11	T	A	1: 107,305,260 (GRCm39)	M212K	probably damaging	Het
Tbc1d22a	C	A	15: 86,183,885 (GRCm39)	T248K	probably damaging	Het
Tcerg1	C	T	18: 42,701,679 (GRCm39)		probably benign	Het
Tpst1	T	A	5: 130,130,627 (GRCm39)	H32Q	probably damaging	Het
Tsc2	A	T	17: 24,818,600 (GRCm39)	V1412E	possibly damaging	Het
Usp19	C	A	9: 108,378,514 (GRCm39)	P1326Q	possibly damaging	Het
Vmn1r235	T	A	17: 21,482,596 (GRCm39)	M307K	probably damaging	Het
Vmn2r58	T	A	7: 41,487,048 (GRCm39)	T616S	probably damaging	Het
Vps13a	G	A	19: 16,637,863 (GRCm39)	T2406I	possibly damaging	Het
Zbtb26	T	A	2: 37,326,053 (GRCm39)	M328L	probably benign	Het
Zp2	A	G	7: 119,736,423 (GRCm39)	F340S	probably 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
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
R1837:Rpap1	UTSW	2	119,600,366 (GRCm39)	critical splice donor site	probably null
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'- ATCTGTCAGCAGCCACGTTCTC -3'
(R):5'- GCCCTAATACCAACCAGTCTTTGCC -3'

Sequencing Primer
(F):5'- CTTCCCTCTGAACATAGAGAGGTG -3'
(R):5'- CCTTTAGCTTTCAGGCACTAAAGAAG -3'

Posted On

2013-04-12