Mutagenetix > Incidental Mutations

Incidental Mutation 'R1920:Tcof1'

213007

Institutional Source

Beutler Lab

Gene Symbol

Tcof1

Ensembl Gene

ENSMUSG00000024613

Gene Name

treacle ribosome biogenesis factor 1

Synonyms

treacle

MMRRC Submission

039938-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1920 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

60813755-60848971 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 60838855 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 127 (T127A)

Ref Sequence

ENSEMBL: ENSMUSP00000134755 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000163446] [ENSMUST00000175934] [ENSMUST00000176630] [ENSMUST00000177172] [ENSMUST00000177343]

Predicted Effect

probably benign
Transcript: ENSMUST00000163446
AA Change: T127A

PolyPhen 2 Score 0.423 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000130454
Gene: ENSMUSG00000024613
AA Change: T127A

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

possibly damaging
Transcript: ENSMUST00000175934
AA Change: T127A

PolyPhen 2 Score 0.635 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000135639
Gene: ENSMUSG00000024613
AA Change: T127A

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

possibly damaging
Transcript: ENSMUST00000176630
AA Change: T127A

PolyPhen 2 Score 0.869 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000135476
Gene: ENSMUSG00000024613
AA Change: T127A

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

possibly damaging
Transcript: ENSMUST00000177172
AA Change: T127A

PolyPhen 2 Score 0.869 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000134755
Gene: ENSMUSG00000024613
AA Change: T127A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000177343
AA Change: T111A

PolyPhen 2 Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000135295
Gene: ENSMUSG00000024613
AA Change: T111A

Domain	Start	End	E-Value	Type
low complexity region	59	93	N/A	INTRINSIC

Meta Mutation Damage Score

0.052

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.7%
20x: 93.4%

Validation Efficiency

98% (101/103)

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700056E22Rik	A	G	1: 184,033,631	V77A	probably benign	Het
Actl7a	G	A	4: 56,744,135	V221M	probably damaging	Het
Alkbh2	C	T	5: 114,124,226	E148K	probably damaging	Het
Arhgef10	C	T	8: 14,956,987		probably benign	Het
Asgr2	T	C	11: 70,098,297	L86P	possibly damaging	Het
Atp12a	A	G	14: 56,386,851	R919G	probably benign	Het
Atrn	A	G	2: 130,995,051	Y1145C	probably damaging	Het
B3gnt5	T	G	16: 19,769,544	L171R	probably benign	Het
Bbof1	T	A	12: 84,411,085	N41K	possibly damaging	Het
Bdp1	A	T	13: 100,098,589	W166R	probably benign	Het
Bean1	A	T	8: 104,211,110	H107L	possibly damaging	Het
Brd4	T	C	17: 32,198,086		probably benign	Het
Cadps	T	C	14: 12,465,859	K1017R	possibly damaging	Het
Cep78	G	A	19: 15,974,351		probably benign	Het
Cfap70	C	T	14: 20,394,952	A1087T	probably damaging	Het
Cideb	A	G	14: 55,755,243	V72A	probably benign	Het
Cpz	T	C	5: 35,517,668	E79G	probably damaging	Het
Crybg1	A	G	10: 43,997,548	L1188P	probably damaging	Het
Cuzd1	G	A	7: 131,309,696	P518L	probably benign	Het
Cyp2j5	A	T	4: 96,663,254	N77K	probably damaging	Het
Cyp4f39	T	G	17: 32,483,291	F254C	probably benign	Het
Dkk1	C	A	19: 30,547,331	V225L	probably damaging	Het
Dlg5	T	C	14: 24,176,571	Y421C	probably damaging	Het
Dll3	T	C	7: 28,298,923	T206A	probably benign	Het
Dnhd1	T	C	7: 105,713,407	C3766R	probably benign	Het
Dock9	G	T	14: 121,583,380	S1534Y	probably damaging	Het
Dst	T	C	1: 34,161,029	V96A	probably damaging	Het
F2r	A	G	13: 95,604,190	F279S	probably damaging	Het
Fam208b	A	T	13: 3,576,612	Y1113N	possibly damaging	Het
Farp1	C	A	14: 121,255,496	N503K	probably benign	Het
Fbxw2	G	A	2: 34,822,764	T95I	probably damaging	Het
Fis1	A	G	5: 136,965,607	T50A	probably benign	Het
Frzb	T	G	2: 80,446,428	E138A	probably damaging	Het
Fsip2	A	T	2: 82,986,820	D4299V	probably benign	Het
Fyco1	C	T	9: 123,830,413	D233N	probably damaging	Het
Gm14548	G	C	7: 3,897,872	P20R	probably damaging	Het
Gmpr	A	G	13: 45,514,521		probably benign	Het
Hc	C	T	2: 35,029,395		probably benign	Het
Hnrnpa1	T	C	15: 103,242,272	M186T	possibly damaging	Het
Kl	A	G	5: 150,982,667	K501E	probably benign	Het
Klhl42	A	G	6: 147,107,929	N422S	probably damaging	Het
Kmt2d	C	G	15: 98,855,590	K127N	probably damaging	Het
Kmt2d	T	A	15: 98,855,591	K127M	probably damaging	Het
Krt39	T	A	11: 99,514,635	T480S	probably benign	Het
Lims2	T	A	18: 31,955,342	C198*	probably null	Het
Mctp1	A	G	13: 76,384,610	N26D	possibly damaging	Het
Mdm4	A	G	1: 133,003,800	S168P	probably benign	Het
Myo3a	A	G	2: 22,564,996	Y71C	probably benign	Het
Nlrp9c	T	A	7: 26,384,894	D420V	probably damaging	Het
Ntf3	A	T	6: 126,102,522	I7N	possibly damaging	Het
Olfr1113	G	A	2: 87,213,377	G162S	probably benign	Het
Olfr1224-ps1	A	G	2: 89,156,581	V198A	probably benign	Het
Olfr272	G	T	4: 52,910,849	T315K	probably benign	Het
Olfr885	T	C	9: 38,061,685	Y122H	probably damaging	Het
Papln	C	A	12: 83,789,254	Y1222*	probably null	Het
Pgm3	T	G	9: 86,558,478	I387L	possibly damaging	Het
Pkd1	C	A	17: 24,595,157	P4167Q	probably damaging	Het
Plcb4	T	A	2: 136,013,027	V1174E	probably damaging	Het
Polr1b	A	G	2: 129,101,111	N9D	probably benign	Het
Prkaa2	G	A	4: 105,036,753	Q456*	probably null	Het
Ptch2	G	T	4: 117,108,661	V425L	probably benign	Het
Ptprh	A	T	7: 4,549,395	S957T	probably benign	Het
Riok1	A	G	13: 38,057,201	D444G	probably benign	Het
Rrbp1	A	T	2: 143,988,291	V652E	probably benign	Het
Rrp36	C	T	17: 46,672,745	R47Q	possibly damaging	Het
Sec24c	T	C	14: 20,686,887	S304P	probably damaging	Het
Serpinb6b	A	T	13: 32,975,008	D64V	possibly damaging	Het
Serpinb9b	A	T	13: 33,039,548		probably null	Het
Six6	T	A	12: 72,941,764	I237N	probably damaging	Het
Slc25a36	A	T	9: 97,093,082	M127K	probably benign	Het
Slc2a10	A	G	2: 165,514,630	D70G	probably damaging	Het
Slc2a3	T	A	6: 122,736,741	I171F	probably damaging	Het
Smc4	A	G	3: 69,033,068	T1087A	probably damaging	Het
Spg21	A	G	9: 65,484,497	Y242C	probably damaging	Het
St14	A	G	9: 31,089,870	V855A	possibly damaging	Het
Stx2	G	A	5: 128,988,839	T251M	probably damaging	Het
Svs3b	A	T	2: 164,255,928	S158T	probably benign	Het
Synpo	C	T	18: 60,603,589	M428I	probably benign	Het
Tbc1d31	G	A	15: 57,912,364	R17H	probably damaging	Het
Tbl3	G	A	17: 24,704,503	T284I	probably benign	Het
Tgoln1	T	C	6: 72,616,101	E132G	probably benign	Het
Timeless	T	C	10: 128,241,714	I221T	probably damaging	Het
Tmem176b	C	T	6: 48,838,204	A52T	possibly damaging	Het
Tmem192	C	T	8: 64,965,583	L207F	probably damaging	Het
Trank1	T	C	9: 111,347,928		probably null	Het
Ttc7b	C	T	12: 100,415,130		probably null	Het
Tubb5	T	C	17: 35,835,298	Y340C	probably benign	Het
Ubr1	G	A	2: 120,930,968	T576I	probably benign	Het
Vcan	T	C	13: 89,693,015	E1470G	probably damaging	Het
Vmn1r200	T	A	13: 22,395,493	N146K	probably damaging	Het
Vmn2r120	T	A	17: 57,524,839	I317F	probably benign	Het
Vmn2r61	T	C	7: 42,300,286	I710T	possibly damaging	Het
Wipf1	T	A	2: 73,440,155	K61N	probably benign	Het
Zfp112	T	C	7: 24,125,237	V210A	probably benign	Het
Zfp612	G	A	8: 110,088,463	V101M	probably benign	Het
Zfp637	A	G	6: 117,845,720	R270G	probably damaging	Het
Zfp652	A	G	11: 95,764,025	E418G	possibly damaging	Het
Zfp97	A	G	17: 17,145,003	I255V	probably benign	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
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
R2229:Tcof1	UTSW	18	60832177	intron	probably benign
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	intron	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

Predicted Primers

PCR Primer
(F):5'- CACAGTGTTCAGTCCTGACC -3'
(R):5'- GATGACAAACCAGTGGACTGTG -3'

Sequencing Primer
(F):5'- CCAGACTTGGCAGTGGGTC -3'
(R):5'- CTGTGAAAGGCCAGAGCTG -3'

Posted On

2014-07-14