Mutagenetix > Incidental Mutation

Incidental Mutation 'R9776:Rpap1'

733678

Institutional Source

Beutler Lab

Gene Symbol

Rpap1

Ensembl Gene

ENSMUSG00000034032

Gene Name

RNA polymerase II associated protein 1

Synonyms

A730023M06Rik, 1190005L06Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.965) question?

Stock #

R9776 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

119594440-119618018 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 119607278 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 287 (V287A)

Ref Sequence

ENSEMBL: ENSMUSP00000037275 (fasta)

Gene Model

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

AlphaFold

Q80TE0

Predicted Effect

probably benign
Transcript: ENSMUST00000048493
AA Change: V287A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000037275
Gene: ENSMUSG00000034032
AA Change: V287A

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 benign
Transcript: ENSMUST00000099529
AA Change: V287A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000097127
Gene: ENSMUSG00000034032
AA Change: V287A

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: ENSMUST00000110793
AA Change: V287A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000106420
Gene: ENSMUSG00000034032
AA Change: V287A

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

probably benign
Transcript: ENSMUST00000184294
AA Change: V287A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000138873
Gene: ENSMUSG00000034032
AA Change: V287A

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

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 99.4%
20x: 98.5%

Validation Efficiency

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700069L16Rik	T	G	5: 113,861,765 (GRCm39)	Q35P	unknown	Het
2010109A12Rik	T	A	5: 93,361,305 (GRCm39)	*120K	probably null	Het
2700049A03Rik	A	G	12: 71,235,448 (GRCm39)	T1133A	possibly damaging	Het
A830005F24Rik	G	A	13: 48,667,758 (GRCm39)	R20Q	unknown	Het
Acta2	T	C	19: 34,223,481 (GRCm39)	T205A	probably benign	Het
Adcy5	A	G	16: 35,100,725 (GRCm39)	D759G	probably damaging	Het
Ankk1	T	A	9: 49,330,714 (GRCm39)	M276L	probably benign	Het
Arfgef2	G	A	2: 166,713,447 (GRCm39)	E1283K	probably damaging	Het
Arhgef26	G	T	3: 62,246,803 (GRCm39)		probably benign	Het
Arhgef28	A	C	13: 98,133,415 (GRCm39)	S351A	probably benign	Het
Arih2	C	T	9: 108,484,504 (GRCm39)	G436S	probably damaging	Het
Bptf	T	C	11: 106,969,396 (GRCm39)	T1013A	probably damaging	Het
Camsap1	A	T	2: 25,828,166 (GRCm39)	V1186E	probably benign	Het
Capn10	G	T	1: 92,871,586 (GRCm39)	A395S	possibly damaging	Het
Ccdc184	A	T	15: 98,066,737 (GRCm39)	T181S	probably damaging	Het
Clasp1	T	C	1: 118,509,108 (GRCm39)	I1345T	possibly damaging	Het
Cpsf1	A	T	15: 76,486,779 (GRCm39)	H252Q	probably damaging	Het
Ctnna2	T	A	6: 77,582,172 (GRCm39)	M363L	probably benign	Het
Cyp24a1	G	A	2: 170,338,625 (GRCm39)	P24S	probably benign	Het
D130040H23Rik	A	G	8: 69,755,566 (GRCm39)	H341R	probably damaging	Het
Dclk3	A	G	9: 111,298,226 (GRCm39)	E590G	probably damaging	Het
Ear2	A	T	14: 44,340,729 (GRCm39)	Y129F	probably benign	Het
Egf	A	G	3: 129,530,514 (GRCm39)	L216P	probably damaging	Het
Fbxw9	T	A	8: 85,792,523 (GRCm39)	H319Q	probably damaging	Het
Gipr	A	G	7: 18,891,487 (GRCm39)	S397P	probably damaging	Het
Gxylt2	G	T	6: 100,682,072 (GRCm39)	E90*	probably null	Het
Hnf1b	T	C	11: 83,784,283 (GRCm39)	V473A	probably benign	Het
Iffo1	G	A	6: 125,130,436 (GRCm39)	E475K	probably damaging	Het
Ifi206	T	A	1: 173,308,075 (GRCm39)	R640S		Het
Ipmk	A	G	10: 71,217,439 (GRCm39)	S328G	probably damaging	Het
Kcnq1	A	T	7: 142,737,368 (GRCm39)	I229F	probably damaging	Het
Kif9	C	A	9: 110,350,398 (GRCm39)	T763N	probably benign	Het
Klhl36	C	T	8: 120,601,129 (GRCm39)	Q383*	probably null	Het
Lrp4	G	T	2: 91,316,179 (GRCm39)	V766F	probably damaging	Het
Mettl26	T	A	17: 26,094,511 (GRCm39)	M3K	probably benign	Het
Muc16	T	A	9: 18,570,675 (GRCm39)	I615F	unknown	Het
Myo7b	T	A	18: 32,133,068 (GRCm39)	Q427L	probably benign	Het
Naip1	A	G	13: 100,559,584 (GRCm39)	M1140T	probably benign	Het
Ncapg	G	A	5: 45,829,834 (GRCm39)	V179I	probably damaging	Het
Nme4	C	T	17: 26,314,410 (GRCm39)	G6E	possibly damaging	Het
Nr1h4	T	C	10: 89,319,311 (GRCm39)	Y185C	probably damaging	Het
Nt5c3b	T	C	11: 100,327,012 (GRCm39)	I95V	probably benign	Het
Ntaq1	A	G	15: 58,004,913 (GRCm39)	T9A	probably benign	Het
Or2y3	C	T	17: 38,393,470 (GRCm39)	R133H	probably benign	Het
Or5g9	A	T	2: 85,552,145 (GRCm39)	Y132F	probably damaging	Het
Or5t16	A	T	2: 86,819,055 (GRCm39)	I155N	probably damaging	Het
Pappa2	G	T	1: 158,611,481 (GRCm39)	P1494Q	probably damaging	Het
Pdzd2	A	G	15: 12,457,909 (GRCm39)	F144S	probably benign	Het
Phactr3	A	G	2: 177,975,896 (GRCm39)	H547R	probably damaging	Het
Pik3c2b	T	A	1: 133,018,588 (GRCm39)	S1012T	possibly damaging	Het
Plppr2	G	A	9: 21,859,107 (GRCm39)	G408D	probably damaging	Het
Pom121	T	A	5: 135,420,554 (GRCm39)	N289I	unknown	Het
Ppa1	T	A	10: 61,487,362 (GRCm39)	S30T	probably damaging	Het
Rgs5	A	T	1: 169,518,089 (GRCm39)	K108*	probably null	Het
Ryr1	A	G	7: 28,774,664 (GRCm39)	Y2326H	probably damaging	Het
Ryr2	A	G	13: 11,707,599 (GRCm39)	S2813P	probably damaging	Het
Sap25	T	C	5: 137,640,702 (GRCm39)		probably null	Het
Senp5	T	C	16: 31,782,279 (GRCm39)	Y739C	probably damaging	Het
Slc25a29	A	T	12: 108,793,017 (GRCm39)	L187Q	possibly damaging	Het
Slc7a2	C	T	8: 41,358,641 (GRCm39)	T328M	probably damaging	Het
Slc7a8	T	C	14: 55,018,759 (GRCm39)	N9S	probably benign	Het
Snx18	A	G	13: 113,754,039 (GRCm39)	V298A	probably benign	Het
Spo11	T	A	2: 172,833,904 (GRCm39)	I342N	possibly damaging	Het
Ssc5d	A	G	7: 4,932,367 (GRCm39)	K344E	probably benign	Het
Sspo	A	T	6: 48,439,269 (GRCm39)	D1639V	probably benign	Het
Stk32b	T	C	5: 37,617,001 (GRCm39)	D285G	probably benign	Het
Sult1b1	T	C	5: 87,662,815 (GRCm39)	D295G	probably benign	Het
Syt5	A	G	7: 4,544,831 (GRCm39)	L274P	probably damaging	Het
Tas1r2	T	C	4: 139,396,208 (GRCm39)	S545P	possibly damaging	Het
Tbc1d17	T	G	7: 44,490,696 (GRCm39)	D632A	probably damaging	Het
Tbc1d2	A	G	4: 46,650,007 (GRCm39)	S10P	probably benign	Het
Tlk1	A	T	2: 70,555,908 (GRCm39)	I417N	probably damaging	Het
Tmem184a	C	T	5: 139,791,984 (GRCm39)	R348H	possibly damaging	Het
Togaram2	T	A	17: 72,023,508 (GRCm39)	V808D	possibly damaging	Het
Tpr	A	G	1: 150,324,939 (GRCm39)	Q2397R	probably benign	Het
Trav7-4	A	G	14: 53,698,994 (GRCm39)	D47G	possibly damaging	Het
Usp17le	T	A	7: 104,419,814 (GRCm39)	M35L	probably benign	Het
Vegfc	C	T	8: 54,633,829 (GRCm39)	S262L	probably benign	Het
Vmn2r74	T	A	7: 85,605,212 (GRCm39)	I479L	possibly damaging	Het
Vps13a	A	T	19: 16,736,958 (GRCm39)	F126L	probably benign	Het
Zfp945	C	A	17: 23,070,582 (GRCm39)	C460F	possibly damaging	Het
Zmym4	G	T	4: 126,804,942 (GRCm39)	S439R	possibly damaging	Het
Zscan4-ps3	A	G	7: 11,344,093 (GRCm39)	E17G	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
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
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
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'- ATCAGCAGGCTGGGTCAAAG -3'
(R):5'- AAGTAGTTTGTCTGGACCTTAGCAC -3'

Sequencing Primer
(F):5'- ATTCCAGGGATCTAACTCAGGCTG -3'
(R):5'- TCTGGACCTTAGCACCCAGAG -3'

Posted On

2022-11-14