Mutagenetix > Incidental Mutation

Incidental Mutation 'R2229:Tcof1'

239640

Institutional Source

Beutler Lab

Gene Symbol

Tcof1

Ensembl Gene

ENSMUSG00000024613

Gene Name

treacle ribosome biogenesis factor 1

Synonyms

treacle

MMRRC Submission

040230-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2229 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

60813755-60848971 bp(-) (GRCm38)

Type of Mutation

intron

DNA Base Change (assembly)

A to G at 60832177 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000134755 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000163446] [ENSMUST00000175934] [ENSMUST00000176630] [ENSMUST00000177172]

AlphaFold

O08784

Predicted Effect

unknown
Transcript: ENSMUST00000163446
AA Change: S547P

SMART Domains

Protein: ENSMUSP00000130454
Gene: ENSMUSG00000024613
AA Change: S547P

Domain	Start	End	E-Value	Type
LisH	6	38	5.09e-4	SMART
Pfam:Treacle	108	322	2.2e-8	PFAM
Pfam:Treacle	321	793	4.6e-204	PFAM
low complexity region	819	834	N/A	INTRINSIC
low complexity region	855	874	N/A	INTRINSIC
low complexity region	879	893	N/A	INTRINSIC
low complexity region	916	927	N/A	INTRINSIC
low complexity region	967	977	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000175934
AA Change: S547P

SMART Domains

Protein: ENSMUSP00000135639
Gene: ENSMUSG00000024613
AA Change: S547P

Domain	Start	End	E-Value	Type
LisH	6	38	5.09e-4	SMART
low complexity region	75	109	N/A	INTRINSIC
Pfam:Treacle	153	329	1.6e-12	PFAM
Pfam:Treacle	321	792	6.1e-175	PFAM
Pfam:Treacle	782	936	3.2e-16	PFAM
low complexity region	969	982	N/A	INTRINSIC
low complexity region	1025	1039	N/A	INTRINSIC
low complexity region	1060	1074	N/A	INTRINSIC
low complexity region	1149	1172	N/A	INTRINSIC
low complexity region	1260	1285	N/A	INTRINSIC
coiled coil region	1306	1335	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176088

Predicted Effect

unknown
Transcript: ENSMUST00000176630
AA Change: S547P

SMART Domains

Protein: ENSMUSP00000135476
Gene: ENSMUSG00000024613
AA Change: S547P

Domain	Start	End	E-Value	Type
LisH	6	38	5.09e-4	SMART
Pfam:Treacle	108	323	2.5e-8	PFAM
Pfam:Treacle	321	793	5.9e-204	PFAM
low complexity region	819	834	N/A	INTRINSIC
low complexity region	843	857	N/A	INTRINSIC
low complexity region	880	891	N/A	INTRINSIC
low complexity region	933	946	N/A	INTRINSIC
low complexity region	989	1003	N/A	INTRINSIC
low complexity region	1024	1038	N/A	INTRINSIC
low complexity region	1113	1136	N/A	INTRINSIC
low complexity region	1224	1249	N/A	INTRINSIC
coiled coil region	1270	1299	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000177172

SMART Domains

Protein: ENSMUSP00000134755
Gene: ENSMUSG00000024613

Domain	Start	End	E-Value	Type
LisH	6	38	5.09e-4	SMART
low complexity region	75	109	N/A	INTRINSIC
Pfam:Treacle	150	322	1.3e-10	PFAM
Pfam:Treacle	321	506	1.5e-78	PFAM
Pfam:Treacle	498	745	2e-105	PFAM
low complexity region	771	786	N/A	INTRINSIC
low complexity region	795	809	N/A	INTRINSIC
low complexity region	832	843	N/A	INTRINSIC
low complexity region	885	898	N/A	INTRINSIC
low complexity region	941	955	N/A	INTRINSIC
low complexity region	976	990	N/A	INTRINSIC

Meta Mutation Damage Score

0.0933

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.1%

Validation Efficiency

99% (78/79)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been associated with Treacher Collins syndrome, a disorder which includes abnormal craniofacial development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
PHENOTYPE: Heterozygotes for a targeted null mutation die perinatally with severe craniofacial malformations including agenesis of the nasal passages, abnormal development of the maxilla, exencephaly, and anophthalmia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam24	A	T	8: 40,680,365	I291L	probably benign	Het
Adcy8	C	A	15: 64,822,207	R407L	possibly damaging	Het
Adgb	A	T	10: 10,436,051	V212E	probably damaging	Het
Adgrg7	C	T	16: 56,752,403	S350N	probably benign	Het
Agbl1	A	G	7: 76,433,378	T448A	probably benign	Het
Aldh1l1	C	G	6: 90,583,186	T605R	probably damaging	Het
Arfip1	A	T	3: 84,547,973	N18K	probably damaging	Het
Atp6v1b2	C	A	8: 69,102,759		probably null	Het
Banp	G	A	8: 121,978,685	S98N	probably damaging	Het
Btnl9	T	C	11: 49,169,118	D601G	probably damaging	Het
C9	T	C	15: 6,445,420	I20T	possibly damaging	Het
Cacna1b	A	G	2: 24,685,804	V744A	probably damaging	Het
Catsper3	A	G	13: 55,808,054	E311G	probably damaging	Het
Ccdc180	G	T	4: 45,948,856		probably null	Het
Cdc5l	A	G	17: 45,407,846	Y615H	probably benign	Het
Crybg2	TGGAGGAGGAGGAGGAGGAG	TGGAGGAGGAGGAGGAG	4: 134,074,526		probably benign	Het
Eml4	C	T	17: 83,451,056	P502S	probably benign	Het
Fsip1	T	C	2: 118,222,444	E367G	probably benign	Het
Gja3	T	C	14: 57,036,714	D67G	probably damaging	Het
Gm4894	T	C	9: 49,274,190		probably benign	Het
Gm7853	A	G	14: 36,089,527		noncoding transcript	Het
Gmps	T	G	3: 64,014,263	Y562*	probably null	Het
Golga2	C	A	2: 32,306,465	P976T	probably benign	Het
Gpr182	T	A	10: 127,750,141	I314F	possibly damaging	Het
Gprc6a	A	G	10: 51,626,795	V324A	possibly damaging	Het
Gykl1	A	G	18: 52,695,267	T516A	probably benign	Het
Hist2h2ab	T	C	3: 96,220,106	L64P	possibly damaging	Het
Ifit1bl2	G	T	19: 34,619,230	L329M	possibly damaging	Het
Igsf9b	T	C	9: 27,333,496	S920P	probably damaging	Het
Kif3c	T	A	12: 3,366,671	S231T	probably benign	Het
Kpna7	A	T	5: 144,989,697	Y482N	probably damaging	Het
Lmnb2	T	C	10: 80,904,392		probably benign	Het
Lrrc69	T	C	4: 14,773,694	S121G	probably benign	Het
Mppe1	A	G	18: 67,228,011		probably null	Het
Muc5b	T	A	7: 141,861,644	C2776S	possibly damaging	Het
Myh8	T	G	11: 67,308,348	N1893K	probably damaging	Het
Myo7a	T	C	7: 98,054,910	T1932A	probably benign	Het
Nbn	A	G	4: 15,970,904	T296A	probably benign	Het
Nckap1l	T	C	15: 103,455,934		probably null	Het
Nek5	A	T	8: 22,113,632	N151K	possibly damaging	Het
Nup93	C	T	8: 94,304,191	T305I	probably benign	Het
Oca2	T	A	7: 56,357,155	H663Q	probably benign	Het
Optn	T	A	2: 5,024,117	H525L	probably damaging	Het
Pdzph1	A	G	17: 58,932,412		probably benign	Het
Pikfyve	A	G	1: 65,267,855	K1801E	probably damaging	Het
Pkd2l2	G	A	18: 34,430,329	V478M	probably damaging	Het
Pmepa1	G	A	2: 173,228,133	R210W	probably damaging	Het
Ppp1r3c	C	A	19: 36,733,698	R224L	probably benign	Het
Prpf19	A	G	19: 10,897,598	T39A	probably benign	Het
Pwwp2b	T	C	7: 139,255,188	C182R	probably damaging	Het
Rcan3	T	C	4: 135,425,377	D11G	probably benign	Het
Rgsl1	C	A	1: 153,822,358	W482L	possibly damaging	Het
Sfxn4	C	T	19: 60,851,020	G200E	probably damaging	Het
Slc4a8	T	C	15: 100,809,299	I848T	probably damaging	Het
Slc7a13	T	C	4: 19,839,399	V334A	probably benign	Het
Smarcc2	A	G	10: 128,488,341		probably benign	Het
Spata18	A	T	5: 73,666,901	I156L	possibly damaging	Het
Spats2	T	C	15: 99,174,453		probably null	Het
Tas2r104	G	A	6: 131,685,132	H205Y	probably damaging	Het
Tex15	C	A	8: 33,571,237	H232N	probably benign	Het
Tg	A	T	15: 66,674,011	Q194L	probably damaging	Het
Tnfrsf22	C	T	7: 143,644,776		probably null	Het
Trim25	T	A	11: 89,016,621	V602E	probably damaging	Het
Ttll9	A	G	2: 152,983,063	E54G	probably damaging	Het
Ttn	T	C	2: 76,729,324	T29578A	probably damaging	Het
Tubgcp5	A	G	7: 55,830,881	Q960R	probably damaging	Het
Ugcg	C	T	4: 59,207,798	P46S	probably benign	Het
Usp13	A	G	3: 32,917,551	I727V	probably benign	Het
Vmn2r67	T	A	7: 85,152,042	I229F	probably benign	Het
Vmn2r92	A	C	17: 18,167,392	I220L	probably benign	Het
Wnk4	T	A	11: 101,275,641		probably benign	Het
Wwp1	A	T	4: 19,641,745	Y437N	probably damaging	Het
Zdhhc5	A	G	2: 84,690,213	I540T	probably damaging	Het
Zfp729b	T	C	13: 67,595,265	I60M	probably damaging	Het

Other mutations in Tcof1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00468:Tcof1	APN	18	60814568	unclassified	probably benign
IGL01339:Tcof1	APN	18	60818095	utr 3 prime	probably benign
IGL02072:Tcof1	APN	18	60831565	missense	possibly damaging	0.85
IGL02160:Tcof1	APN	18	60848743	unclassified	probably benign
IGL02513:Tcof1	APN	18	60831778	missense	possibly damaging	0.51
IGL02823:Tcof1	APN	18	60816048	missense	probably benign	0.00
IGL03161:Tcof1	APN	18	60833488	missense	possibly damaging	0.86
IGL03291:Tcof1	APN	18	60829061	missense	possibly damaging	0.71
FR4304:Tcof1	UTSW	18	60835742	unclassified	probably benign
FR4589:Tcof1	UTSW	18	60828650	critical splice donor site	probably benign
FR4737:Tcof1	UTSW	18	60828650	critical splice donor site	probably benign
PIT4802001:Tcof1	UTSW	18	60831938	missense	unknown
R0569:Tcof1	UTSW	18	60829035	missense	possibly damaging	0.85
R0602:Tcof1	UTSW	18	60833533	missense	probably damaging	1.00
R0744:Tcof1	UTSW	18	60845832	missense	probably damaging	1.00
R0782:Tcof1	UTSW	18	60816280	missense	probably damaging	0.97
R0833:Tcof1	UTSW	18	60845832	missense	probably damaging	1.00
R0836:Tcof1	UTSW	18	60845832	missense	probably damaging	1.00
R0885:Tcof1	UTSW	18	60835850	missense	possibly damaging	0.84
R1465:Tcof1	UTSW	18	60818954	splice site	probably benign
R1528:Tcof1	UTSW	18	60814999	nonsense	probably null
R1643:Tcof1	UTSW	18	60816228	missense	possibly damaging	0.72
R1919:Tcof1	UTSW	18	60816084	missense	possibly damaging	0.85
R1920:Tcof1	UTSW	18	60838855	missense	possibly damaging	0.87
R1921:Tcof1	UTSW	18	60838855	missense	possibly damaging	0.87
R2023:Tcof1	UTSW	18	60833533	missense	probably damaging	1.00
R2108:Tcof1	UTSW	18	60835773	missense	probably damaging	0.97
R2114:Tcof1	UTSW	18	60832785	missense	possibly damaging	0.85
R2115:Tcof1	UTSW	18	60832785	missense	possibly damaging	0.85
R2116:Tcof1	UTSW	18	60832785	missense	possibly damaging	0.85
R2117:Tcof1	UTSW	18	60832785	missense	possibly damaging	0.85
R2156:Tcof1	UTSW	18	60831829	missense	possibly damaging	0.92
R2221:Tcof1	UTSW	18	60837901	missense	possibly damaging	0.51
R2913:Tcof1	UTSW	18	60816084	missense	possibly damaging	0.85
R2914:Tcof1	UTSW	18	60816084	missense	possibly damaging	0.85
R3944:Tcof1	UTSW	18	60822837	missense	probably damaging	0.98
R3979:Tcof1	UTSW	18	60831533	missense	possibly damaging	0.71
R4049:Tcof1	UTSW	18	60832903	missense	possibly damaging	0.84
R4125:Tcof1	UTSW	18	60819601	missense	unknown
R5047:Tcof1	UTSW	18	60831914	missense	possibly damaging	0.86
R5433:Tcof1	UTSW	18	60818033	utr 3 prime	probably benign
R5546:Tcof1	UTSW	18	60831556	missense	possibly damaging	0.85
R5832:Tcof1	UTSW	18	60819539	missense	unknown
R5965:Tcof1	UTSW	18	60833418	critical splice donor site	probably null
R6301:Tcof1	UTSW	18	60828825	missense	probably damaging	0.97
R6480:Tcof1	UTSW	18	60814780	splice site	probably null
R6910:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R6911:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R7105:Tcof1	UTSW	18	60843296	missense	probably damaging	1.00
R7225:Tcof1	UTSW	18	60828448	missense	unknown
R7356:Tcof1	UTSW	18	60818094	missense	unknown
R7467:Tcof1	UTSW	18	60831905	missense	unknown
R7536:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R7804:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R7818:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R7863:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8006:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8007:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8008:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8063:Tcof1	UTSW	18	60838762	missense	probably damaging	1.00
R8192:Tcof1	UTSW	18	60843303	missense	probably damaging	1.00
R8200:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8203:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8204:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8207:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8217:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8300:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8517:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8518:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8553:Tcof1	UTSW	18	60831571	missense	possibly damaging	0.92
R8729:Tcof1	UTSW	18	60829073	missense	unknown
R8732:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R8749:Tcof1	UTSW	18	60829051	missense	possibly damaging	0.84
R9800:Tcof1	UTSW	18	60816486	missense	unknown
RF001:Tcof1	UTSW	18	60835739	unclassified	probably benign
RF007:Tcof1	UTSW	18	60833568	small insertion	probably benign
RF009:Tcof1	UTSW	18	60835743	unclassified	probably benign
RF010:Tcof1	UTSW	18	60835744	unclassified	probably benign
RF011:Tcof1	UTSW	18	60835739	unclassified	probably benign
RF013:Tcof1	UTSW	18	60835743	unclassified	probably benign
RF015:Tcof1	UTSW	18	60833584	small insertion	probably benign
RF016:Tcof1	UTSW	18	60833575	small insertion	probably benign
RF022:Tcof1	UTSW	18	60835735	unclassified	probably benign
RF024:Tcof1	UTSW	18	60835738	unclassified	probably benign
RF027:Tcof1	UTSW	18	60835736	unclassified	probably benign
RF029:Tcof1	UTSW	18	60835735	unclassified	probably benign
RF029:Tcof1	UTSW	18	60835745	unclassified	probably benign
RF030:Tcof1	UTSW	18	60833568	small insertion	probably benign
RF030:Tcof1	UTSW	18	60833574	small insertion	probably benign
RF030:Tcof1	UTSW	18	60835723	unclassified	probably benign
RF031:Tcof1	UTSW	18	60833565	small insertion	probably benign
RF031:Tcof1	UTSW	18	60835745	unclassified	probably benign
RF035:Tcof1	UTSW	18	60833553	small insertion	probably benign
RF036:Tcof1	UTSW	18	60828408	small insertion	probably benign
RF036:Tcof1	UTSW	18	60835736	unclassified	probably benign
RF038:Tcof1	UTSW	18	60833566	small insertion	probably benign
RF040:Tcof1	UTSW	18	60828408	small insertion	probably benign
RF040:Tcof1	UTSW	18	60833583	small insertion	probably benign
RF041:Tcof1	UTSW	18	60833572	small insertion	probably benign
RF041:Tcof1	UTSW	18	60833576	small insertion	probably benign
RF043:Tcof1	UTSW	18	60833572	small insertion	probably benign
RF050:Tcof1	UTSW	18	60833579	small insertion	probably benign
RF051:Tcof1	UTSW	18	60833579	small insertion	probably benign
RF053:Tcof1	UTSW	18	60835747	unclassified	probably benign
RF056:Tcof1	UTSW	18	60833575	small insertion	probably benign
RF057:Tcof1	UTSW	18	60833564	small insertion	probably benign
RF057:Tcof1	UTSW	18	60833565	small insertion	probably benign
RF057:Tcof1	UTSW	18	60833566	small insertion	probably benign
RF057:Tcof1	UTSW	18	60833571	small insertion	probably benign
RF060:Tcof1	UTSW	18	60835744	unclassified	probably benign
RF060:Tcof1	UTSW	18	60835747	unclassified	probably benign
RF063:Tcof1	UTSW	18	60833573	small insertion	probably benign
RF064:Tcof1	UTSW	18	60833571	small insertion	probably benign
RF064:Tcof1	UTSW	18	60833574	small insertion	probably benign

Predicted Primers

PCR Primer
(F):5'- AAGCTTTCATCTGCTTTTCCAGAG -3'
(R):5'- CTGGGTCTCTAATTGCTGCCTG -3'

Sequencing Primer
(F):5'- CTTAGCCTGTGGAGAAAGTGC -3'
(R):5'- TGCCTGTCTCCTACCTGGGG -3'

Posted On

2014-10-15