Mutagenetix > Incidental Mutation

Incidental Mutation 'R0452:Rfc1'

39667

Institutional Source

Beutler Lab

Gene Symbol

Rfc1

Ensembl Gene

ENSMUSG00000029191

Gene Name

replication factor C (activator 1) 1

Synonyms

140kDa, Recc1, Alp145, RFC140

MMRRC Submission

038652-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0452 (G1)

Quality Score

203

Status

Validated

Chromosome

Chromosomal Location

65261850-65335670 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 65264297 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 1086 (D1086E)

Ref Sequence

ENSEMBL: ENSMUSP00000144980 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041892] [ENSMUST00000172732] [ENSMUST00000203471] [ENSMUST00000203581] [ENSMUST00000203596] [ENSMUST00000203653] [ENSMUST00000204965]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000041892

SMART Domains

Protein: ENSMUSP00000038098
Gene: ENSMUSG00000037890

Domain	Start	End	E-Value	Type
WD40	6	42	4.26e1	SMART
WD40	44	83	2.13e1	SMART
WD40	85	125	2.75e1	SMART
WD40	128	166	2.67e-1	SMART
Blast:WD40	220	258	6e-9	BLAST
WD40	264	302	1.46e-1	SMART
Blast:WD40	308	347	2e-18	BLAST
Pfam:WD40_3	508	564	2.7e-32	PFAM
low complexity region	1103	1116	N/A	INTRINSIC
low complexity region	1259	1268	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000172732
AA Change: D1085E

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000134444
Gene: ENSMUSG00000029191
AA Change: D1085E

Domain	Start	End	E-Value	Type
low complexity region	31	44	N/A	INTRINSIC
low complexity region	79	93	N/A	INTRINSIC
low complexity region	139	152	N/A	INTRINSIC
low complexity region	308	325	N/A	INTRINSIC
low complexity region	342	360	N/A	INTRINSIC
BRCT	401	479	7.39e-17	SMART
low complexity region	484	502	N/A	INTRINSIC
AAA	627	762	9.65e-10	SMART
Pfam:RFC1	899	1052	5.2e-62	PFAM
low complexity region	1104	1132	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000172780
AA Change: D1099E

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000133738
Gene: ENSMUSG00000029191
AA Change: D1099E

Domain	Start	End	E-Value	Type
low complexity region	31	44	N/A	INTRINSIC
low complexity region	79	93	N/A	INTRINSIC
low complexity region	139	152	N/A	INTRINSIC
low complexity region	322	339	N/A	INTRINSIC
low complexity region	356	374	N/A	INTRINSIC
BRCT	415	493	7.39e-17	SMART
low complexity region	498	516	N/A	INTRINSIC
AAA	640	775	9.65e-10	SMART
Pfam:RFC1	912	1065	2.6e-61	PFAM
low complexity region	1117	1145	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203359

Predicted Effect

probably benign
Transcript: ENSMUST00000203471
AA Change: D1086E

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000144954
Gene: ENSMUSG00000029191
AA Change: D1086E

Domain	Start	End	E-Value	Type
low complexity region	31	44	N/A	INTRINSIC
low complexity region	79	93	N/A	INTRINSIC
low complexity region	139	152	N/A	INTRINSIC
low complexity region	308	325	N/A	INTRINSIC
low complexity region	342	360	N/A	INTRINSIC
BRCT	401	479	7.39e-17	SMART
low complexity region	484	502	N/A	INTRINSIC
AAA	627	762	9.65e-10	SMART
Pfam:RFC1	899	1052	2.5e-61	PFAM
low complexity region	1104	1132	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000203554

Predicted Effect

probably benign
Transcript: ENSMUST00000203581
AA Change: D1099E

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000145385
Gene: ENSMUSG00000029191
AA Change: D1099E

Domain	Start	End	E-Value	Type
low complexity region	31	44	N/A	INTRINSIC
low complexity region	79	93	N/A	INTRINSIC
low complexity region	139	152	N/A	INTRINSIC
low complexity region	322	339	N/A	INTRINSIC
low complexity region	356	374	N/A	INTRINSIC
BRCT	415	493	7.39e-17	SMART
low complexity region	498	516	N/A	INTRINSIC
AAA	640	775	9.65e-10	SMART
Pfam:RFC1	912	1065	2.6e-61	PFAM
low complexity region	1117	1145	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000203596
AA Change: D171E

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000145181
Gene: ENSMUSG00000029191
AA Change: D171E

Domain	Start	End	E-Value	Type
Pfam:RFC1	2	137	1.7e-46	PFAM
low complexity region	189	212	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000203653

SMART Domains

Protein: ENSMUSP00000144866
Gene: ENSMUSG00000037890

Domain	Start	End	E-Value	Type
WD40	6	42	4.26e1	SMART
WD40	44	83	2.13e1	SMART
WD40	85	125	2.75e1	SMART
WD40	128	166	2.67e-1	SMART
Blast:WD40	220	258	6e-9	BLAST
WD40	264	302	1.46e-1	SMART
Blast:WD40	308	347	2e-18	BLAST
Pfam:WD40_3	508	564	2.7e-32	PFAM
low complexity region	1103	1116	N/A	INTRINSIC
low complexity region	1259	1268	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000204965
AA Change: D1086E

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000144980
Gene: ENSMUSG00000029191
AA Change: D1086E

Domain	Start	End	E-Value	Type
low complexity region	31	44	N/A	INTRINSIC
low complexity region	79	93	N/A	INTRINSIC
low complexity region	139	152	N/A	INTRINSIC
low complexity region	308	325	N/A	INTRINSIC
low complexity region	342	360	N/A	INTRINSIC
BRCT	401	479	7.39e-17	SMART
low complexity region	484	502	N/A	INTRINSIC
AAA	627	762	9.65e-10	SMART
Pfam:RFC1	899	1052	2.5e-61	PFAM
low complexity region	1104	1131	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205063

Meta Mutation Damage Score

0.0635

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.7%

Validation Efficiency

99% (93/94)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the large subunit of replication factor C, a five subunit DNA polymerase accessory protein, which is a DNA-dependent ATPase required for eukaryotic DNA replication and repair. The large subunit acts as an activator of DNA polymerases, binds to the 3' end of primers, and promotes coordinated synthesis of both strands. It may also have a role in telomere stability. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2011]

Allele List at MGI

Other mutations in this stock

Total: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6030452D12Rik	A	G	8: 106,507,190		probably benign	Het
Acap3	C	A	4: 155,902,328	S347*	probably null	Het
Acvr1	G	A	2: 58,500,495	P19L	probably benign	Het
Add2	G	T	6: 86,104,629	E366*	probably null	Het
Ankrd28	C	A	14: 31,748,738	A153S	probably damaging	Het
Anxa8	A	T	14: 34,094,770	I206F	probably damaging	Het
Arhgef4	G	A	1: 34,732,322	E1237K	probably damaging	Het
Arid1a	C	T	4: 133,689,105	A1120T	unknown	Het
Atad5	T	C	11: 80,106,421	V857A	probably damaging	Het
Atp2a3	T	A	11: 72,977,232		probably null	Het
Atxn1l	C	T	8: 109,732,395	V412I	possibly damaging	Het
Card11	A	G	5: 140,880,370	S923P	probably benign	Het
Cars	C	A	7: 143,592,625	E21*	probably null	Het
Ccdc115	A	G	1: 34,437,621		probably benign	Het
Ccnj	T	A	19: 40,845,064		probably null	Het
Cds2	C	T	2: 132,298,479	T182I	probably damaging	Het
Ceacam14	A	G	7: 17,815,323	H213R	probably benign	Het
Cfap44	A	T	16: 44,431,945	M806L	probably benign	Het
Chd8	A	T	14: 52,214,587	I1317K	probably damaging	Het
Cherp	A	T	8: 72,461,522		probably benign	Het
Creb5	C	G	6: 53,604,542	T30S	possibly damaging	Het
Csf2ra	A	G	19: 61,226,895	M94T	probably benign	Het
Cyp2b19	A	C	7: 26,766,762	D330A	probably benign	Het
Ddost	G	A	4: 138,310,188	V188M	possibly damaging	Het
Dnah7a	A	T	1: 53,605,819	D1019E	probably benign	Het
Dtx1	A	T	5: 120,694,992	I127N	possibly damaging	Het
Dyrk2	T	C	10: 118,868,763	T3A	possibly damaging	Het
Elovl5	C	T	9: 77,960,911	T35M	probably damaging	Het
Emc7	T	C	2: 112,466,969		probably benign	Het
Erp27	T	C	6: 136,909,489	Y182C	probably damaging	Het
Exoc2	T	A	13: 30,886,327		probably benign	Het
F5	A	C	1: 164,185,107	D530A	probably damaging	Het
Fam149a	A	T	8: 45,355,649	V149E	probably damaging	Het
Fbxo41	A	G	6: 85,478,182	S614P	probably damaging	Het
Fmn1	T	A	2: 113,636,779	Y1342N	possibly damaging	Het
Gm10334	A	G	6: 41,445,337	Y45H	probably benign	Het
Gpr22	T	A	12: 31,708,794	D443V	possibly damaging	Het
Il17rd	T	A	14: 27,091,931	W56R	probably damaging	Het
Itga2b	A	T	11: 102,465,953		probably null	Het
Jmjd1c	T	C	10: 67,255,482	M2514T	probably benign	Het
Klk9	T	C	7: 43,794,251		probably benign	Het
Krr1	T	C	10: 111,975,598	Y66H	probably damaging	Het
Lamb2	T	C	9: 108,486,354		probably benign	Het
Lgals3bp	A	T	11: 118,393,464	Y430N	probably benign	Het
Lrp10	T	C	14: 54,467,579	V113A	probably benign	Het
Mgam	A	G	6: 40,759,090	Y841C	probably damaging	Het
Nisch	T	A	14: 31,177,464		probably benign	Het
Nlrp4d	G	A	7: 10,378,292	T650I	probably benign	Het
Olfr1314	T	A	2: 112,092,636	K22*	probably null	Het
Olfr506	C	T	7: 108,612,370	T21I	possibly damaging	Het
Parp4	A	G	14: 56,648,843	D1793G	unknown	Het
Pcm1	A	G	8: 41,325,905	D1850G	probably benign	Het
Pgap2	G	A	7: 102,236,462	A145T	probably damaging	Het
Phc1	G	A	6: 122,323,036	A583V	probably damaging	Het
Plcd3	G	A	11: 103,071,259		probably benign	Het
Ppm1m	T	A	9: 106,197,302	Q214L	probably damaging	Het
Prkg2	A	G	5: 98,997,520		probably benign	Het
Rasal3	T	C	17: 32,395,817		probably benign	Het
Rnf145	T	A	11: 44,561,760	L522H	probably damaging	Het
Setd2	T	A	9: 110,553,100		probably null	Het
Sik1	C	A	17: 31,849,081	V377F	possibly damaging	Het
Slc44a4	T	C	17: 34,928,095	I367T	possibly damaging	Het
Slfn3	A	G	11: 83,213,128	D275G	possibly damaging	Het
Smarcad1	A	T	6: 65,074,822	N313I	possibly damaging	Het
Smc4	A	T	3: 69,008,028	K138*	probably null	Het
Smg6	T	A	11: 74,930,213	S437T	probably benign	Het
Spaca9	G	T	2: 28,695,993	Q20K	probably damaging	Het
Spatc1	T	G	15: 76,268,293	I41S	probably damaging	Het
Spink5	A	T	18: 43,963,318	T5S	possibly damaging	Het
St3gal1	C	A	15: 67,109,655		probably benign	Het
Stat5a	C	A	11: 100,863,135	T97K	probably benign	Het
Stat5b	A	T	11: 100,798,330	I246N	probably benign	Het
Supt6	G	T	11: 78,227,003	D462E	probably damaging	Het
Swi5	A	T	2: 32,281,824		probably benign	Het
Syne1	A	T	10: 5,405,435	V375E	probably damaging	Het
Tcp1	T	C	17: 12,924,352	F516S	probably benign	Het
Tdrd7	A	T	4: 45,965,488		probably benign	Het
Tgfbr3	A	T	5: 107,140,423	N457K	probably benign	Het
Tmem209	A	G	6: 30,487,381	M500T	probably damaging	Het
Tmem44	C	T	16: 30,517,463		probably benign	Het
Ttc21a	T	A	9: 119,939,154		probably benign	Het
Ttn	T	A	2: 76,836,003	I88F	possibly damaging	Het
Ttn	A	G	2: 76,871,110		probably benign	Het
Ube2w	T	C	1: 16,602,255		probably benign	Het
Ufc1	C	T	1: 171,289,954		probably benign	Het
Uhmk1	A	G	1: 170,212,402	M132T	possibly damaging	Het
Usp29	A	G	7: 6,963,182	N675D	possibly damaging	Het
Vmn1r23	A	G	6: 57,926,484	V103A	possibly damaging	Het
Wdr59	G	T	8: 111,521,972	R4S	possibly damaging	Het
Zc3hav1	T	A	6: 38,307,437	E914D	probably benign	Het

Other mutations in Rfc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00551:Rfc1	APN	5	65296009	missense	probably benign	0.00
IGL00909:Rfc1	APN	5	65279699	missense	probably benign	0.00
IGL01791:Rfc1	APN	5	65263145	missense	probably benign	0.00
IGL01884:Rfc1	APN	5	65274460	missense	possibly damaging	0.94
IGL02737:Rfc1	APN	5	65311163	missense	possibly damaging	0.82
Disturbing	UTSW	5	65266162	missense	probably damaging	1.00
P0038:Rfc1	UTSW	5	65287961	missense	probably damaging	1.00
R0317:Rfc1	UTSW	5	65296052	splice site	probably null
R0699:Rfc1	UTSW	5	65319399	splice site	probably null
R0945:Rfc1	UTSW	5	65278709	critical splice donor site	probably null
R1192:Rfc1	UTSW	5	65293911	missense	probably benign	0.03
R1341:Rfc1	UTSW	5	65291194	missense	probably damaging	1.00
R1425:Rfc1	UTSW	5	65319518	missense	probably damaging	1.00
R1551:Rfc1	UTSW	5	65277363	missense	probably damaging	0.99
R1800:Rfc1	UTSW	5	65264379	missense	probably damaging	1.00
R1969:Rfc1	UTSW	5	65319524	missense	probably damaging	1.00
R2006:Rfc1	UTSW	5	65311054	nonsense	probably null
R2026:Rfc1	UTSW	5	65288029	missense	probably damaging	1.00
R2073:Rfc1	UTSW	5	65301939	missense	probably damaging	0.98
R2137:Rfc1	UTSW	5	65311039	critical splice donor site	probably null
R2330:Rfc1	UTSW	5	65312969	missense	possibly damaging	0.94
R3774:Rfc1	UTSW	5	65264406	missense	probably damaging	1.00
R3787:Rfc1	UTSW	5	65296014	missense	probably benign	0.00
R4920:Rfc1	UTSW	5	65287928	missense	probably damaging	1.00
R5055:Rfc1	UTSW	5	65266162	missense	probably damaging	1.00
R5308:Rfc1	UTSW	5	65279461	missense	probably damaging	0.99
R5723:Rfc1	UTSW	5	65277426	missense	probably null	0.78
R5729:Rfc1	UTSW	5	65277452	missense	probably damaging	1.00
R5844:Rfc1	UTSW	5	65293787	missense	probably benign	0.19
R6045:Rfc1	UTSW	5	65279549	missense	probably damaging	1.00
R6484:Rfc1	UTSW	5	65293677	missense	probably benign	0.01
R6495:Rfc1	UTSW	5	65273815	splice site	probably null
R6531:Rfc1	UTSW	5	65312979	missense	possibly damaging	0.92
R6717:Rfc1	UTSW	5	65302004	nonsense	probably null
R6717:Rfc1	UTSW	5	65312961	missense	probably damaging	0.97
R6845:Rfc1	UTSW	5	65311116	missense	possibly damaging	0.53
R6880:Rfc1	UTSW	5	65277386	missense	probably benign	0.14
R7329:Rfc1	UTSW	5	65263135	missense	unknown
R7331:Rfc1	UTSW	5	65311044	missense	probably damaging	1.00
R7466:Rfc1	UTSW	5	65275426	missense	probably damaging	1.00
R7497:Rfc1	UTSW	5	65279498	missense	probably damaging	1.00
R7588:Rfc1	UTSW	5	65272507	missense	probably damaging	1.00
R8020:Rfc1	UTSW	5	65272178	missense	probably damaging	1.00
R8056:Rfc1	UTSW	5	65294093	intron	probably benign
R8282:Rfc1	UTSW	5	65268946	critical splice donor site	probably null
R8316:Rfc1	UTSW	5	65278734	missense	probably benign	0.05
R8320:Rfc1	UTSW	5	65303036	nonsense	probably null
R8865:Rfc1	UTSW	5	65278792	missense	possibly damaging	0.89
R8968:Rfc1	UTSW	5	65275435	missense	probably benign	0.03
R8997:Rfc1	UTSW	5	65275721	missense	probably damaging	1.00
R9454:Rfc1	UTSW	5	65274431	missense
R9476:Rfc1	UTSW	5	65279799	missense	probably damaging	0.99
R9631:Rfc1	UTSW	5	65272508	missense	probably damaging	1.00
R9758:Rfc1	UTSW	5	65302048	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- ACGCTGTAAAATACACCTGTGGCTT -3'
(R):5'- TGTGCAGCACTCACAACCTCTC -3'

Sequencing Primer
(F):5'- acataacggcacacatctaaaac -3'
(R):5'- CTTCTCTTTCTTTAGGTGAAAGCG -3'

Posted On

2013-05-23