Mutagenetix > Incidental Mutation

Incidental Mutation 'R4049:Tcof1'

314073

Institutional Source

Beutler Lab

Gene Symbol

Tcof1

Ensembl Gene

ENSMUSG00000024613

Gene Name

treacle ribosome biogenesis factor 1

Synonyms

treacle

MMRRC Submission

041616-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4049 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

60813755-60848971 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 60832903 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 376 (A376S)

Ref Sequence

ENSEMBL: ENSMUSP00000130454 (fasta)

Gene Model

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

AlphaFold

O08784

Predicted Effect

possibly damaging
Transcript: ENSMUST00000163446
AA Change: A376S

PolyPhen 2 Score 0.837 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000130454
Gene: ENSMUSG00000024613
AA Change: A376S

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: A376S

SMART Domains

Protein: ENSMUSP00000135639
Gene: ENSMUSG00000024613
AA Change: A376S

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: A376S

SMART Domains

Protein: ENSMUSP00000135476
Gene: ENSMUSG00000024613
AA Change: A376S

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

unknown
Transcript: ENSMUST00000177172
AA Change: A376S

SMART Domains

Protein: ENSMUSP00000134755
Gene: ENSMUSG00000024613
AA Change: A376S

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

0.1795

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.6%

Validation Efficiency

100% (65/65)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb5	T	A	12: 118,868,669 (GRCm38)	E1190V	probably damaging	Het
Arhgef10	A	G	8: 14,979,998 (GRCm38)	T928A	probably benign	Het
Arhgef10l	T	A	4: 140,515,451 (GRCm38)	I836F	probably benign	Het
Blm	T	A	7: 80,502,862 (GRCm38)	T446S	probably benign	Het
Ccdc63	T	A	5: 122,122,750 (GRCm38)	Q237L	probably damaging	Het
Cep57l1	G	T	10: 41,729,360 (GRCm38)	R130S	probably damaging	Het
Clstn2	T	G	9: 97,457,560 (GRCm38)	E786A	possibly damaging	Het
Col16a1	C	T	4: 130,068,752 (GRCm38)	P540L	probably damaging	Het
Csf2	A	G	11: 54,249,333 (GRCm38)	F61L	probably damaging	Het
Ctr9	C	T	7: 111,055,543 (GRCm38)	R1094C	unknown	Het
Cyp3a41a	A	G	5: 145,713,540 (GRCm38)	C98R	probably damaging	Het
Dthd1	T	A	5: 62,827,165 (GRCm38)	C404*	probably null	Het
Egfem1	A	C	3: 29,686,731 (GRCm38)	H518P	probably benign	Het
Elf3	T	C	1: 135,254,277 (GRCm38)	S369G	probably benign	Het
Eml6	C	T	11: 29,838,577 (GRCm38)	V503M	probably damaging	Het
Enthd1	T	C	15: 80,560,039 (GRCm38)	D105G	probably damaging	Het
Eral1	A	G	11: 78,075,602 (GRCm38)	L250P	probably damaging	Het
Gdf15	A	T	8: 70,629,955 (GRCm38)	M167K	probably benign	Het
Ggps1	T	C	13: 14,053,699 (GRCm38)	K300E	probably benign	Het
Gm8074	G	A	9: 78,322,336 (GRCm38)		noncoding transcript	Het
Herc3	A	G	6: 58,876,837 (GRCm38)	I623V	probably damaging	Het
Mad1l1	A	G	5: 140,132,816 (GRCm38)	S457P	probably damaging	Het
Map1lc3a	G	T	2: 155,277,542 (GRCm38)	V91F	possibly damaging	Het
Map4k3	A	G	17: 80,605,965 (GRCm38)	V617A	probably benign	Het
Mov10l1	T	A	15: 88,995,032 (GRCm38)		probably benign	Het
Mroh2a	A	G	1: 88,258,664 (GRCm38)	S64G	probably benign	Het
Ncor1	G	T	11: 62,329,668 (GRCm38)		probably null	Het
Nfe2	C	T	15: 103,250,937 (GRCm38)	E36K	possibly damaging	Het
Olfr1176	T	C	2: 88,343,800 (GRCm38)		probably null	Het
Olfr1212	A	G	2: 88,959,273 (GRCm38)	K269R	probably benign	Het
Olfr1251	T	C	2: 89,667,662 (GRCm38)	I75V	probably benign	Het
Olfr653	T	C	7: 104,580,368 (GRCm38)	F241L	probably benign	Het
Oprm1	G	A	10: 6,829,087 (GRCm38)	V95I	probably benign	Het
Pcdha9	T	A	18: 36,997,942 (GRCm38)	H21Q	probably benign	Het
Pcolce2	A	T	9: 95,638,755 (GRCm38)	I62F	probably damaging	Het
Pfpl	T	A	19: 12,429,689 (GRCm38)	C435S	probably damaging	Het
Pkhd1l1	G	A	15: 44,498,557 (GRCm38)	C542Y	probably damaging	Het
Plekha5	T	C	6: 140,583,871 (GRCm38)	S75P	probably damaging	Het
Pphln1	C	A	15: 93,465,106 (GRCm38)	A202E	probably damaging	Het
Ppp1r1a	A	G	15: 103,532,454 (GRCm38)	L92P	probably damaging	Het
Prokr2	T	C	2: 132,381,494 (GRCm38)	T43A	probably benign	Het
Rai14	T	C	15: 10,592,212 (GRCm38)	N199S	probably benign	Het
Rasgrp2	T	C	19: 6,404,727 (GRCm38)	L199P	probably damaging	Het
Rnf213	A	C	11: 119,482,448 (GRCm38)	M4939L	possibly damaging	Het
Slc23a2	C	T	2: 132,060,683 (GRCm38)	R533Q	probably benign	Het
Slc7a7	T	C	14: 54,373,091 (GRCm38)		probably null	Het
Snrpd2	T	A	7: 19,151,307 (GRCm38)	V31E	probably damaging	Het
Spire1	G	T	18: 67,529,031 (GRCm38)		probably null	Het
Srsf4	T	C	4: 131,900,543 (GRCm38)		probably benign	Het
Tcf20	A	G	15: 82,853,429 (GRCm38)	S1274P	probably damaging	Het
Thsd1	T	A	8: 22,243,164 (GRCm38)	Y76N	possibly damaging	Het
Timm44	A	G	8: 4,260,561 (GRCm38)	V397A	probably benign	Het
Tmc6	G	A	11: 117,778,261 (GRCm38)	T89I	possibly damaging	Het
Trbv31	C	A	6: 41,557,705 (GRCm38)	C107F	probably damaging	Het
Trim37	T	A	11: 87,140,603 (GRCm38)		probably null	Het
Ttll5	T	C	12: 86,012,799 (GRCm38)	V1226A	probably benign	Het
Ube3b	T	C	5: 114,412,870 (GRCm38)	V865A	probably benign	Het
Vmn2r86	A	T	10: 130,447,097 (GRCm38)	M550K	probably damaging	Het
Vps54	C	A	11: 21,300,183 (GRCm38)	T373N	probably benign	Het
Wdr64	T	G	1: 175,805,856 (GRCm38)	I891S	probably benign	Het
Wisp2	A	G	2: 163,828,984 (GRCm38)	D137G	probably damaging	Het
Zfhx4	C	T	3: 5,398,859 (GRCm38)	S1384L	probably damaging	Het
Zfp703	A	G	8: 26,979,085 (GRCm38)	E259G	possibly damaging	Het
Zfp933	T	C	4: 147,826,512 (GRCm38)	H209R	probably damaging	Het
Zfp980	A	G	4: 145,702,600 (GRCm38)	H633R	probably damaging	Het

Other mutations in Tcof1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00468:Tcof1	APN	18	60,814,568 (GRCm38)	unclassified	probably benign
IGL01339:Tcof1	APN	18	60,818,095 (GRCm38)	utr 3 prime	probably benign
IGL02072:Tcof1	APN	18	60,831,565 (GRCm38)	missense	possibly damaging	0.85
IGL02160:Tcof1	APN	18	60,848,743 (GRCm38)	unclassified	probably benign
IGL02513:Tcof1	APN	18	60,831,778 (GRCm38)	missense	possibly damaging	0.51
IGL02823:Tcof1	APN	18	60,816,048 (GRCm38)	missense	probably benign	0.00
IGL03161:Tcof1	APN	18	60,833,488 (GRCm38)	missense	possibly damaging	0.86
IGL03291:Tcof1	APN	18	60,829,061 (GRCm38)	missense	possibly damaging	0.71
FR4304:Tcof1	UTSW	18	60,835,742 (GRCm38)	unclassified	probably benign
FR4589:Tcof1	UTSW	18	60,828,650 (GRCm38)	critical splice donor site	probably benign
FR4737:Tcof1	UTSW	18	60,828,650 (GRCm38)	critical splice donor site	probably benign
PIT4802001:Tcof1	UTSW	18	60,831,938 (GRCm38)	missense	unknown
R0569:Tcof1	UTSW	18	60,829,035 (GRCm38)	missense	possibly damaging	0.85
R0602:Tcof1	UTSW	18	60,833,533 (GRCm38)	missense	probably damaging	1.00
R0744:Tcof1	UTSW	18	60,845,832 (GRCm38)	missense	probably damaging	1.00
R0782:Tcof1	UTSW	18	60,816,280 (GRCm38)	missense	probably damaging	0.97
R0833:Tcof1	UTSW	18	60,845,832 (GRCm38)	missense	probably damaging	1.00
R0836:Tcof1	UTSW	18	60,845,832 (GRCm38)	missense	probably damaging	1.00
R0885:Tcof1	UTSW	18	60,835,850 (GRCm38)	missense	possibly damaging	0.84
R1465:Tcof1	UTSW	18	60,818,954 (GRCm38)	splice site	probably benign
R1528:Tcof1	UTSW	18	60,814,999 (GRCm38)	nonsense	probably null
R1643:Tcof1	UTSW	18	60,816,228 (GRCm38)	missense	possibly damaging	0.72
R1919:Tcof1	UTSW	18	60,816,084 (GRCm38)	missense	possibly damaging	0.85
R1920:Tcof1	UTSW	18	60,838,855 (GRCm38)	missense	possibly damaging	0.87
R1921:Tcof1	UTSW	18	60,838,855 (GRCm38)	missense	possibly damaging	0.87
R2023:Tcof1	UTSW	18	60,833,533 (GRCm38)	missense	probably damaging	1.00
R2108:Tcof1	UTSW	18	60,835,773 (GRCm38)	missense	probably damaging	0.97
R2114:Tcof1	UTSW	18	60,832,785 (GRCm38)	missense	possibly damaging	0.85
R2115:Tcof1	UTSW	18	60,832,785 (GRCm38)	missense	possibly damaging	0.85
R2116:Tcof1	UTSW	18	60,832,785 (GRCm38)	missense	possibly damaging	0.85
R2117:Tcof1	UTSW	18	60,832,785 (GRCm38)	missense	possibly damaging	0.85
R2156:Tcof1	UTSW	18	60,831,829 (GRCm38)	missense	possibly damaging	0.92
R2221:Tcof1	UTSW	18	60,837,901 (GRCm38)	missense	possibly damaging	0.51
R2229:Tcof1	UTSW	18	60,832,177 (GRCm38)	intron	probably benign
R2913:Tcof1	UTSW	18	60,816,084 (GRCm38)	missense	possibly damaging	0.85
R2914:Tcof1	UTSW	18	60,816,084 (GRCm38)	missense	possibly damaging	0.85
R3944:Tcof1	UTSW	18	60,822,837 (GRCm38)	missense	probably damaging	0.98
R3979:Tcof1	UTSW	18	60,831,533 (GRCm38)	missense	possibly damaging	0.71
R4125:Tcof1	UTSW	18	60,819,601 (GRCm38)	missense	unknown
R5047:Tcof1	UTSW	18	60,831,914 (GRCm38)	missense	possibly damaging	0.86
R5433:Tcof1	UTSW	18	60,818,033 (GRCm38)	utr 3 prime	probably benign
R5546:Tcof1	UTSW	18	60,831,556 (GRCm38)	missense	possibly damaging	0.85
R5832:Tcof1	UTSW	18	60,819,539 (GRCm38)	missense	unknown
R5965:Tcof1	UTSW	18	60,833,418 (GRCm38)	critical splice donor site	probably null
R6301:Tcof1	UTSW	18	60,828,825 (GRCm38)	missense	probably damaging	0.97
R6480:Tcof1	UTSW	18	60,814,780 (GRCm38)	splice site	probably null
R6910:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R6911:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R7105:Tcof1	UTSW	18	60,843,296 (GRCm38)	missense	probably damaging	1.00
R7225:Tcof1	UTSW	18	60,828,448 (GRCm38)	missense	unknown
R7356:Tcof1	UTSW	18	60,818,094 (GRCm38)	missense	unknown
R7467:Tcof1	UTSW	18	60,831,905 (GRCm38)	missense	unknown
R7536:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R7804:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R7818:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R7863:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8006:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8007:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8008:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8063:Tcof1	UTSW	18	60,838,762 (GRCm38)	missense	probably damaging	1.00
R8192:Tcof1	UTSW	18	60,843,303 (GRCm38)	missense	probably damaging	1.00
R8200:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8203:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8204:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8207:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8217:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8300:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8517:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8518:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8553:Tcof1	UTSW	18	60,831,571 (GRCm38)	missense	possibly damaging	0.92
R8729:Tcof1	UTSW	18	60,829,073 (GRCm38)	missense	unknown
R8732:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R8749:Tcof1	UTSW	18	60,829,051 (GRCm38)	missense	possibly damaging	0.84
R9800:Tcof1	UTSW	18	60,816,486 (GRCm38)	missense	unknown
RF001:Tcof1	UTSW	18	60,835,739 (GRCm38)	unclassified	probably benign
RF007:Tcof1	UTSW	18	60,833,568 (GRCm38)	small insertion	probably benign
RF009:Tcof1	UTSW	18	60,835,743 (GRCm38)	unclassified	probably benign
RF010:Tcof1	UTSW	18	60,835,744 (GRCm38)	unclassified	probably benign
RF011:Tcof1	UTSW	18	60,835,739 (GRCm38)	unclassified	probably benign
RF013:Tcof1	UTSW	18	60,835,743 (GRCm38)	unclassified	probably benign
RF015:Tcof1	UTSW	18	60,833,584 (GRCm38)	small insertion	probably benign
RF016:Tcof1	UTSW	18	60,833,575 (GRCm38)	small insertion	probably benign
RF022:Tcof1	UTSW	18	60,835,735 (GRCm38)	unclassified	probably benign
RF024:Tcof1	UTSW	18	60,835,738 (GRCm38)	unclassified	probably benign
RF027:Tcof1	UTSW	18	60,835,736 (GRCm38)	unclassified	probably benign
RF029:Tcof1	UTSW	18	60,835,735 (GRCm38)	unclassified	probably benign
RF029:Tcof1	UTSW	18	60,835,745 (GRCm38)	unclassified	probably benign
RF030:Tcof1	UTSW	18	60,835,723 (GRCm38)	unclassified	probably benign
RF030:Tcof1	UTSW	18	60,833,574 (GRCm38)	small insertion	probably benign
RF030:Tcof1	UTSW	18	60,833,568 (GRCm38)	small insertion	probably benign
RF031:Tcof1	UTSW	18	60,835,745 (GRCm38)	unclassified	probably benign
RF031:Tcof1	UTSW	18	60,833,565 (GRCm38)	small insertion	probably benign
RF035:Tcof1	UTSW	18	60,833,553 (GRCm38)	small insertion	probably benign
RF036:Tcof1	UTSW	18	60,835,736 (GRCm38)	unclassified	probably benign
RF036:Tcof1	UTSW	18	60,828,408 (GRCm38)	small insertion	probably benign
RF038:Tcof1	UTSW	18	60,833,566 (GRCm38)	small insertion	probably benign
RF040:Tcof1	UTSW	18	60,833,583 (GRCm38)	small insertion	probably benign
RF040:Tcof1	UTSW	18	60,828,408 (GRCm38)	small insertion	probably benign
RF041:Tcof1	UTSW	18	60,833,576 (GRCm38)	small insertion	probably benign
RF041:Tcof1	UTSW	18	60,833,572 (GRCm38)	small insertion	probably benign
RF043:Tcof1	UTSW	18	60,833,572 (GRCm38)	small insertion	probably benign
RF050:Tcof1	UTSW	18	60,833,579 (GRCm38)	small insertion	probably benign
RF051:Tcof1	UTSW	18	60,833,579 (GRCm38)	small insertion	probably benign
RF053:Tcof1	UTSW	18	60,835,747 (GRCm38)	unclassified	probably benign
RF056:Tcof1	UTSW	18	60,833,575 (GRCm38)	small insertion	probably benign
RF057:Tcof1	UTSW	18	60,833,566 (GRCm38)	small insertion	probably benign
RF057:Tcof1	UTSW	18	60,833,565 (GRCm38)	small insertion	probably benign
RF057:Tcof1	UTSW	18	60,833,564 (GRCm38)	small insertion	probably benign
RF057:Tcof1	UTSW	18	60,833,571 (GRCm38)	small insertion	probably benign
RF060:Tcof1	UTSW	18	60,835,744 (GRCm38)	unclassified	probably benign
RF060:Tcof1	UTSW	18	60,835,747 (GRCm38)	unclassified	probably benign
RF063:Tcof1	UTSW	18	60,833,573 (GRCm38)	small insertion	probably benign
RF064:Tcof1	UTSW	18	60,833,574 (GRCm38)	small insertion	probably benign
RF064:Tcof1	UTSW	18	60,833,571 (GRCm38)	small insertion	probably benign

Predicted Primers

PCR Primer
(F):5'- TTTCTAGGCAGAGCACAAGGC -3'
(R):5'- AACTGGTCCTAACCCCTGTC -3'

Sequencing Primer
(F):5'- TCACCTTGGCAGGACTCGTG -3'
(R):5'- TCCTCAGCTGGGCCCAAC -3'

Posted On

2015-04-30