Mutagenetix > Incidental Mutation

Incidental Mutation 'RF022:Tcof1'

603969

Institutional Source

Beutler Lab

Gene Symbol

Tcof1

Ensembl Gene

ENSMUSG00000024613

Gene Name

treacle ribosome biogenesis factor 1

Synonyms

treacle

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

RF022 (G1)

Quality Score

130.469

Status

Not validated

Chromosome

Chromosomal Location

60946827-60982043 bp(-) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

CAG to CAGTAG at 60968807 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000135295 (fasta)

Gene Model

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

AlphaFold

O08784

Predicted Effect

probably benign
Transcript: ENSMUST00000163446

SMART Domains

Protein: ENSMUSP00000130454
Gene: ENSMUSG00000024613

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

probably benign
Transcript: ENSMUST00000175934

SMART Domains

Protein: ENSMUSP00000135639
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	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

probably benign
Transcript: ENSMUST00000176630

SMART Domains

Protein: ENSMUSP00000135476
Gene: ENSMUSG00000024613

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

Predicted Effect

probably benign
Transcript: ENSMUST00000177343

SMART Domains

Protein: ENSMUSP00000135295
Gene: ENSMUSG00000024613

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

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.3%
20x: 98.5%

Validation Efficiency

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001K19Rik	GTACT	GTACTACT	12: 110,634,877 (GRCm39)		probably null	Het
Acap3	CCTGGGCTGCTG	CCTGGGCTGCTGCATACTGGGCTGCTG	4: 155,989,553 (GRCm39)		probably benign	Het
Adam6b	A	T	12: 113,455,289 (GRCm39)	E702V	possibly damaging	Het
Arpc3	A	G	5: 122,538,489 (GRCm39)	T7A	probably benign	Het
Bcl3	G	A	7: 19,542,966 (GRCm39)	P393L	probably damaging	Het
Ceacam9	A	G	7: 16,459,304 (GRCm39)	D201G	possibly damaging	Het
Chga	AGC	AGCCGC	12: 102,527,679 (GRCm39)		probably benign	Het
Clgn	A	G	8: 84,152,235 (GRCm39)	K579R	probably damaging	Het
Cntnap2	C	T	6: 46,998,599 (GRCm39)	R884W	probably damaging	Het
Col6a4	A	T	9: 105,954,207 (GRCm39)	D377E	probably damaging	Het
Cort	GCCCACTCGT	G	4: 149,209,869 (GRCm39)		probably benign	Het
D5Ertd579e	A	C	5: 36,772,006 (GRCm39)	I796M	probably damaging	Het
Dmkn	GGTGGAAGTGGTGGAAG	GGTGGAAGTGGTGGAAGAGGTGGAAGTCGTGGAAGTGGTGGAAG	7: 30,466,600 (GRCm39)		probably benign	Het
Dpagt1	G	T	9: 44,243,262 (GRCm39)	V266L	possibly damaging	Het
Ebf3	C	A	7: 136,915,671 (GRCm39)		probably benign	Het
Exd2	AGCAGCCGCAGCC	AGCAGCC	12: 80,522,691 (GRCm39)		probably benign	Het
Flywch1	CACTCCTGGTGT	CACTCCTGGTGTGGGGAGGCTACGTACTCACCAACTCCTGGTGT	17: 23,981,141 (GRCm39)		probably null	Het
Gab3	CTT	CTTATT	X: 74,043,600 (GRCm39)		probably null	Het
Golga4	A	G	9: 118,387,057 (GRCm39)	D1393G	probably damaging	Het
Gpc5	G	A	14: 115,789,688 (GRCm39)	V521I	probably damaging	Het
Grik1	A	T	16: 87,693,225 (GRCm39)	N859K		Het
Insrr	G	A	3: 87,711,792 (GRCm39)	A511T	possibly damaging	Het
Isx	A	G	8: 75,600,474 (GRCm39)	D69G	probably damaging	Het
Kcnh8	G	A	17: 53,285,267 (GRCm39)	R1079H	probably benign	Het
Lkaaear1	CAGCTCCAG	CAGCTCCAGGTCGAGCTCCAG	2: 181,339,370 (GRCm39)		probably benign	Het
Lrch1	TTGGTGGTGCTGGTGG	TTGGTGG	14: 75,185,014 (GRCm39)		probably benign	Het
Magel2	A	G	7: 62,029,841 (GRCm39)	E915G	unknown	Het
Maml3	A	G	3: 51,764,083 (GRCm39)	S294P	probably damaging	Het
Mamld1	AGC	AGCCGC	X: 70,162,426 (GRCm39)		probably benign	Het
Mef2d	A	T	3: 88,075,574 (GRCm39)	T486S	probably benign	Het
Ms4a8a	A	G	19: 11,053,689 (GRCm39)	V139A	possibly damaging	Het
Ogfr	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	2: 180,237,059 (GRCm39)		probably benign	Het
Or2z8	T	G	8: 72,812,468 (GRCm39)	*315G	probably null	Het
Pdik1l	GTTTTTGTTTT	GTTTTTGTTTTTTTTTTGTTTT	4: 134,006,678 (GRCm39)		probably null	Het
Pnma8a	TCATGATGCACCTGCTTCAACATC	TCATGATGCACCTGCTTCAACATCGCATGATGCACCTGCTTCAACATC	7: 16,695,352 (GRCm39)		probably benign	Het
Ppfibp2	T	C	7: 107,296,817 (GRCm39)	L177P	probably damaging	Het
Ppp1r13l	ACAGGCACCCTGCTCCGGC	AC	7: 19,102,467 (GRCm39)		probably benign	Het
Ptprh	A	G	7: 4,552,367 (GRCm39)	F966L	probably benign	Het
Rad17	A	G	13: 100,773,593 (GRCm39)	L132S	probably damaging	Het
Raph1	GG	GGGGG	1: 60,528,426 (GRCm39)		probably benign	Het
Rnf126	AGGACGAGG	AG	10: 79,594,977 (GRCm39)		probably null	Het
Rwdd2b	C	T	16: 87,233,558 (GRCm39)	A181T	probably benign	Het
Sh3pxd2b	GCCTGT	GCCTGTTCCTGT	11: 32,373,054 (GRCm39)		probably benign	Het
Six3	CGG	CGGTGG	17: 85,928,784 (GRCm39)		probably benign	Het
Sla	C	T	15: 66,654,593 (GRCm39)	G231D	probably benign	Het
Tfeb	GCA	GCAACA	17: 48,097,019 (GRCm39)		probably benign	Het
Tgm5	T	A	2: 120,902,092 (GRCm39)	E192D	probably damaging	Het
Tmem123	A	G	9: 7,791,414 (GRCm39)	Y171C	probably damaging	Het
Tnrc18	G	A	5: 142,759,385 (GRCm39)	A999V		Het
Triobp	C	T	15: 78,858,482 (GRCm39)	P1361L	probably benign	Het
Ubac1	A	T	2: 25,895,470 (GRCm39)	W328R	probably damaging	Het
Ube2q1	A	G	3: 89,688,200 (GRCm39)	N324S	probably benign	Het
Zcchc2	T	C	1: 105,939,472 (GRCm39)	I407T	possibly damaging	Het
Zfp384	GCCCAGGCCCAGGCCCAGGCCCAG	GCCCAGGCCCAGCCCCAGGCCCAGGCCCAGGCCCAG	6: 125,013,434 (GRCm39)		probably benign	Het

Other mutations in Tcof1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00468:Tcof1	APN	18	60,947,640 (GRCm39)	unclassified	probably benign
IGL01339:Tcof1	APN	18	60,951,167 (GRCm39)	utr 3 prime	probably benign
IGL02072:Tcof1	APN	18	60,964,637 (GRCm39)	missense	possibly damaging	0.85
IGL02160:Tcof1	APN	18	60,981,815 (GRCm39)	unclassified	probably benign
IGL02513:Tcof1	APN	18	60,964,850 (GRCm39)	missense	possibly damaging	0.51
IGL02823:Tcof1	APN	18	60,949,120 (GRCm39)	missense	probably benign	0.00
IGL03161:Tcof1	APN	18	60,966,560 (GRCm39)	missense	possibly damaging	0.86
IGL03291:Tcof1	APN	18	60,962,133 (GRCm39)	missense	possibly damaging	0.71
FR4304:Tcof1	UTSW	18	60,968,814 (GRCm39)	unclassified	probably benign
FR4589:Tcof1	UTSW	18	60,961,722 (GRCm39)	critical splice donor site	probably benign
FR4737:Tcof1	UTSW	18	60,961,722 (GRCm39)	critical splice donor site	probably benign
PIT4802001:Tcof1	UTSW	18	60,965,010 (GRCm39)	missense	unknown
R0569:Tcof1	UTSW	18	60,962,107 (GRCm39)	missense	possibly damaging	0.85
R0602:Tcof1	UTSW	18	60,966,605 (GRCm39)	missense	probably damaging	1.00
R0744:Tcof1	UTSW	18	60,978,904 (GRCm39)	missense	probably damaging	1.00
R0782:Tcof1	UTSW	18	60,949,352 (GRCm39)	missense	probably damaging	0.97
R0833:Tcof1	UTSW	18	60,978,904 (GRCm39)	missense	probably damaging	1.00
R0836:Tcof1	UTSW	18	60,978,904 (GRCm39)	missense	probably damaging	1.00
R0885:Tcof1	UTSW	18	60,968,922 (GRCm39)	missense	possibly damaging	0.84
R1465:Tcof1	UTSW	18	60,952,026 (GRCm39)	splice site	probably benign
R1528:Tcof1	UTSW	18	60,948,071 (GRCm39)	nonsense	probably null
R1643:Tcof1	UTSW	18	60,949,300 (GRCm39)	missense	possibly damaging	0.72
R1919:Tcof1	UTSW	18	60,949,156 (GRCm39)	missense	possibly damaging	0.85
R1920:Tcof1	UTSW	18	60,971,927 (GRCm39)	missense	possibly damaging	0.87
R1921:Tcof1	UTSW	18	60,971,927 (GRCm39)	missense	possibly damaging	0.87
R2023:Tcof1	UTSW	18	60,966,605 (GRCm39)	missense	probably damaging	1.00
R2108:Tcof1	UTSW	18	60,968,845 (GRCm39)	missense	probably damaging	0.97
R2114:Tcof1	UTSW	18	60,965,857 (GRCm39)	missense	possibly damaging	0.85
R2115:Tcof1	UTSW	18	60,965,857 (GRCm39)	missense	possibly damaging	0.85
R2116:Tcof1	UTSW	18	60,965,857 (GRCm39)	missense	possibly damaging	0.85
R2117:Tcof1	UTSW	18	60,965,857 (GRCm39)	missense	possibly damaging	0.85
R2156:Tcof1	UTSW	18	60,964,901 (GRCm39)	missense	possibly damaging	0.92
R2221:Tcof1	UTSW	18	60,970,973 (GRCm39)	missense	possibly damaging	0.51
R2229:Tcof1	UTSW	18	60,965,249 (GRCm39)	intron	probably benign
R2913:Tcof1	UTSW	18	60,949,156 (GRCm39)	missense	possibly damaging	0.85
R2914:Tcof1	UTSW	18	60,949,156 (GRCm39)	missense	possibly damaging	0.85
R3944:Tcof1	UTSW	18	60,955,909 (GRCm39)	missense	probably damaging	0.98
R3979:Tcof1	UTSW	18	60,964,605 (GRCm39)	missense	possibly damaging	0.71
R4049:Tcof1	UTSW	18	60,965,975 (GRCm39)	missense	possibly damaging	0.84
R4125:Tcof1	UTSW	18	60,952,673 (GRCm39)	missense	unknown
R5047:Tcof1	UTSW	18	60,964,986 (GRCm39)	missense	possibly damaging	0.86
R5433:Tcof1	UTSW	18	60,951,105 (GRCm39)	utr 3 prime	probably benign
R5546:Tcof1	UTSW	18	60,964,628 (GRCm39)	missense	possibly damaging	0.85
R5832:Tcof1	UTSW	18	60,952,611 (GRCm39)	missense	unknown
R5965:Tcof1	UTSW	18	60,966,490 (GRCm39)	critical splice donor site	probably null
R6301:Tcof1	UTSW	18	60,961,897 (GRCm39)	missense	probably damaging	0.97
R6480:Tcof1	UTSW	18	60,947,852 (GRCm39)	splice site	probably null
R6910:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R6911:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R7105:Tcof1	UTSW	18	60,976,368 (GRCm39)	missense	probably damaging	1.00
R7225:Tcof1	UTSW	18	60,961,520 (GRCm39)	missense	unknown
R7356:Tcof1	UTSW	18	60,951,166 (GRCm39)	missense	unknown
R7467:Tcof1	UTSW	18	60,964,977 (GRCm39)	missense	unknown
R7536:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R7804:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R7818:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R7863:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8006:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8007:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8008:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8063:Tcof1	UTSW	18	60,971,834 (GRCm39)	missense	probably damaging	1.00
R8192:Tcof1	UTSW	18	60,976,375 (GRCm39)	missense	probably damaging	1.00
R8200:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8203:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8204:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8207:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8217:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8300:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8517:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8518:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8553:Tcof1	UTSW	18	60,964,643 (GRCm39)	missense	possibly damaging	0.92
R8729:Tcof1	UTSW	18	60,962,145 (GRCm39)	missense	unknown
R8732:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R8749:Tcof1	UTSW	18	60,962,123 (GRCm39)	missense	possibly damaging	0.84
R9800:Tcof1	UTSW	18	60,949,558 (GRCm39)	missense	unknown
RF001:Tcof1	UTSW	18	60,968,811 (GRCm39)	unclassified	probably benign
RF007:Tcof1	UTSW	18	60,966,640 (GRCm39)	small insertion	probably benign
RF009:Tcof1	UTSW	18	60,968,815 (GRCm39)	unclassified	probably benign
RF010:Tcof1	UTSW	18	60,968,816 (GRCm39)	unclassified	probably benign
RF011:Tcof1	UTSW	18	60,968,811 (GRCm39)	unclassified	probably benign
RF013:Tcof1	UTSW	18	60,968,815 (GRCm39)	unclassified	probably benign
RF015:Tcof1	UTSW	18	60,966,656 (GRCm39)	small insertion	probably benign
RF016:Tcof1	UTSW	18	60,966,647 (GRCm39)	small insertion	probably benign
RF024:Tcof1	UTSW	18	60,968,810 (GRCm39)	unclassified	probably benign
RF027:Tcof1	UTSW	18	60,968,808 (GRCm39)	unclassified	probably benign
RF029:Tcof1	UTSW	18	60,968,807 (GRCm39)	unclassified	probably benign
RF029:Tcof1	UTSW	18	60,968,817 (GRCm39)	unclassified	probably benign
RF030:Tcof1	UTSW	18	60,968,795 (GRCm39)	unclassified	probably benign
RF030:Tcof1	UTSW	18	60,966,646 (GRCm39)	small insertion	probably benign
RF030:Tcof1	UTSW	18	60,966,640 (GRCm39)	small insertion	probably benign
RF031:Tcof1	UTSW	18	60,968,817 (GRCm39)	unclassified	probably benign
RF031:Tcof1	UTSW	18	60,966,637 (GRCm39)	small insertion	probably benign
RF035:Tcof1	UTSW	18	60,966,625 (GRCm39)	small insertion	probably benign
RF036:Tcof1	UTSW	18	60,968,808 (GRCm39)	unclassified	probably benign
RF036:Tcof1	UTSW	18	60,961,480 (GRCm39)	small insertion	probably benign
RF038:Tcof1	UTSW	18	60,966,638 (GRCm39)	small insertion	probably benign
RF040:Tcof1	UTSW	18	60,966,655 (GRCm39)	small insertion	probably benign
RF040:Tcof1	UTSW	18	60,961,480 (GRCm39)	small insertion	probably benign
RF041:Tcof1	UTSW	18	60,966,648 (GRCm39)	small insertion	probably benign
RF041:Tcof1	UTSW	18	60,966,644 (GRCm39)	small insertion	probably benign
RF043:Tcof1	UTSW	18	60,966,644 (GRCm39)	small insertion	probably benign
RF050:Tcof1	UTSW	18	60,966,651 (GRCm39)	small insertion	probably benign
RF051:Tcof1	UTSW	18	60,966,651 (GRCm39)	small insertion	probably benign
RF053:Tcof1	UTSW	18	60,968,819 (GRCm39)	unclassified	probably benign
RF056:Tcof1	UTSW	18	60,966,647 (GRCm39)	small insertion	probably benign
RF057:Tcof1	UTSW	18	60,966,638 (GRCm39)	small insertion	probably benign
RF057:Tcof1	UTSW	18	60,966,637 (GRCm39)	small insertion	probably benign
RF057:Tcof1	UTSW	18	60,966,636 (GRCm39)	small insertion	probably benign
RF057:Tcof1	UTSW	18	60,966,643 (GRCm39)	small insertion	probably benign
RF060:Tcof1	UTSW	18	60,968,816 (GRCm39)	unclassified	probably benign
RF060:Tcof1	UTSW	18	60,968,819 (GRCm39)	unclassified	probably benign
RF063:Tcof1	UTSW	18	60,966,645 (GRCm39)	small insertion	probably benign
RF064:Tcof1	UTSW	18	60,966,646 (GRCm39)	small insertion	probably benign
RF064:Tcof1	UTSW	18	60,966,643 (GRCm39)	small insertion	probably benign

Predicted Primers

PCR Primer
(F):5'- CTCTAGAATGGGCCCTCTTCAG -3'
(R):5'- GGAAGGCTCTTCATGTGCTG -3'

Sequencing Primer
(F):5'- AGGAGTTCTCCATCACACAGTGG -3'
(R):5'- CTGCTTCTAGGTGAAATCTCCAG -3'

Posted On

2019-12-04