Mutagenetix > Incidental Mutation

Incidental Mutation 'R0401:Tcf3'

38230

Institutional Source

Beutler Lab

Gene Symbol

Tcf3

Ensembl Gene

ENSMUSG00000020167

Gene Name

transcription factor 3

Synonyms

A1, ALF2, bHLHb21, E12, E2A, E47, Pan1, Pan2, Tcfe2a

MMRRC Submission

038606-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.954) question?

Stock #

R0401 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

80409514-80433647 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 80421158 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 77 (S77R)

Ref Sequence

ENSEMBL: ENSMUSP00000100980 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020377] [ENSMUST00000020379] [ENSMUST00000105339] [ENSMUST00000105340] [ENSMUST00000105341] [ENSMUST00000105342] [ENSMUST00000105343] [ENSMUST00000105344] [ENSMUST00000105345] [ENSMUST00000105346] [ENSMUST00000156244]

AlphaFold

P15806

Predicted Effect

possibly damaging
Transcript: ENSMUST00000020377
AA Change: S77R

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000020377
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	242	265	N/A	INTRINSIC
low complexity region	340	355	N/A	INTRINSIC
low complexity region	462	480	N/A	INTRINSIC
low complexity region	495	506	N/A	INTRINSIC
low complexity region	528	539	N/A	INTRINSIC
HLH	553	606	2.66e-10	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000020379
AA Change: S77R

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000020379
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	241	264	N/A	INTRINSIC
low complexity region	339	354	N/A	INTRINSIC
low complexity region	462	480	N/A	INTRINSIC
low complexity region	495	506	N/A	INTRINSIC
HLH	550	603	8.79e-11	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105339
AA Change: S77R

PolyPhen 2 Score 0.658 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000100976
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	241	264	N/A	INTRINSIC
low complexity region	336	351	N/A	INTRINSIC
low complexity region	458	476	N/A	INTRINSIC
low complexity region	491	502	N/A	INTRINSIC
low complexity region	524	535	N/A	INTRINSIC
HLH	549	602	2.66e-10	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000105340
AA Change: S77R

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000100977
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	241	264	N/A	INTRINSIC
low complexity region	339	354	N/A	INTRINSIC
low complexity region	462	480	N/A	INTRINSIC
low complexity region	495	506	N/A	INTRINSIC
HLH	549	602	8.79e-11	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105341
AA Change: S77R

PolyPhen 2 Score 0.871 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000100978
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	241	264	N/A	INTRINSIC
low complexity region	336	351	N/A	INTRINSIC
low complexity region	458	476	N/A	INTRINSIC
low complexity region	491	502	N/A	INTRINSIC
HLH	546	599	8.79e-11	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105342
AA Change: S77R

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000100979
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	242	265	N/A	INTRINSIC
low complexity region	340	355	N/A	INTRINSIC
low complexity region	463	481	N/A	INTRINSIC
low complexity region	496	507	N/A	INTRINSIC
low complexity region	529	540	N/A	INTRINSIC
HLH	554	607	2.66e-10	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000105343
AA Change: S77R

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000100980
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	242	265	N/A	INTRINSIC
low complexity region	340	355	N/A	INTRINSIC
low complexity region	462	480	N/A	INTRINSIC
low complexity region	495	506	N/A	INTRINSIC
HLH	550	603	8.79e-11	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000105344
AA Change: S77R

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000100981
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	242	265	N/A	INTRINSIC
low complexity region	340	355	N/A	INTRINSIC
low complexity region	463	481	N/A	INTRINSIC
low complexity region	496	507	N/A	INTRINSIC
HLH	551	604	8.79e-11	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105345
AA Change: S77R

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000100982
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	241	264	N/A	INTRINSIC
low complexity region	339	354	N/A	INTRINSIC
low complexity region	461	479	N/A	INTRINSIC
low complexity region	494	505	N/A	INTRINSIC
HLH	549	602	8.79e-11	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000105346
AA Change: S77R

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000100983
Gene: ENSMUSG00000020167
AA Change: S77R

Domain	Start	End	E-Value	Type
low complexity region	55	73	N/A	INTRINSIC
low complexity region	125	148	N/A	INTRINSIC
low complexity region	241	264	N/A	INTRINSIC
low complexity region	339	354	N/A	INTRINSIC
low complexity region	461	479	N/A	INTRINSIC
low complexity region	494	505	N/A	INTRINSIC
low complexity region	527	538	N/A	INTRINSIC
HLH	552	605	2.66e-10	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127931

Predicted Effect

probably damaging
Transcript: ENSMUST00000156244
AA Change: S41R

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000120303
Gene: ENSMUSG00000020167
AA Change: S41R

Domain	Start	End	E-Value	Type
low complexity region	19	37	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000156990
AA Change: S68R

SMART Domains

Protein: ENSMUSP00000121172
Gene: ENSMUSG00000020167
AA Change: S68R

Domain	Start	End	E-Value	Type
low complexity region	47	65	N/A	INTRINSIC
low complexity region	117	140	N/A	INTRINSIC
low complexity region	234	257	N/A	INTRINSIC
low complexity region	329	344	N/A	INTRINSIC
low complexity region	451	469	N/A	INTRINSIC
low complexity region	484	495	N/A	INTRINSIC
HLH	539	592	8.79e-11	SMART

Meta Mutation Damage Score

0.0825

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.6%

Validation Efficiency

98% (90/92)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011]
PHENOTYPE: Homozygotes for targeted null mutations are devoid of mature B cells, have a partial early block in T-lymphocyte development, and show high postnatal mortality. Many survivors develop T-cell lymphomas between 3 and 10 months of age. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	T	3: 138,070,306	H1752L	possibly damaging	Het
8030462N17Rik	C	A	18: 77,673,962	S218I	probably damaging	Het
A530099J19Rik	A	T	13: 19,729,494		noncoding transcript	Het
Abcc5	T	C	16: 20,376,558	K730E	probably benign	Het
Ahnak	A	G	19: 9,015,116	D4588G	probably benign	Het
AI467606	G	A	7: 127,092,436	R61H	probably damaging	Het
Apoa4	T	A	9: 46,243,058	V319E	probably damaging	Het
Atad5	T	A	11: 80,120,699	D1297E	probably benign	Het
BC005624	G	A	2: 30,980,009	T62I	probably benign	Het
Bcl6	T	C	16: 23,972,594	K337E	probably damaging	Het
Cad	T	A	5: 31,073,986		probably benign	Het
Ccdc73	T	C	2: 104,991,289	S528P	probably benign	Het
Ccng2	T	G	5: 93,273,413	C261G	possibly damaging	Het
Cdh11	A	T	8: 102,674,006	I110N	probably damaging	Het
Cgnl1	A	G	9: 71,705,239	V767A	probably damaging	Het
Cit	A	G	5: 115,985,479	T1460A	probably benign	Het
Clec4b2	C	T	6: 123,181,300	Q42*	probably null	Het
Clip1	A	G	5: 123,653,789	V106A	probably damaging	Het
Crb1	T	C	1: 139,198,791		probably benign	Het
Cts6	T	C	13: 61,198,339		probably benign	Het
Cul9	T	C	17: 46,541,704	E244G	probably damaging	Het
Ddx55	A	T	5: 124,567,951	I480F	probably damaging	Het
Dixdc1	A	G	9: 50,693,674	S17P	possibly damaging	Het
Drosha	T	A	15: 12,926,031	Y1235*	probably null	Het
Dsg2	G	T	18: 20,592,508		probably benign	Het
E2f5	T	C	3: 14,579,025		probably null	Het
Epc2	A	G	2: 49,528,974	T265A	probably damaging	Het
Etaa1	T	G	11: 17,947,514	D201A	probably damaging	Het
Fancd2	T	C	6: 113,548,343	I260T	possibly damaging	Het
Fhdc1	G	A	3: 84,444,624	A1098V	probably benign	Het
Gm17689	G	T	9: 36,582,628	A3E	unknown	Het
Gm7030	C	T	17: 36,128,705	V128M	probably damaging	Het
Gpd2	G	A	2: 57,340,093	V286I	possibly damaging	Het
Herc2	A	C	7: 56,157,732	E2523A	probably damaging	Het
Jmjd1c	G	A	10: 67,220,382	R527H	probably damaging	Het
Kif12	G	A	4: 63,169,525		probably benign	Het
Lrp2	A	T	2: 69,479,148	N2802K	probably damaging	Het
Mab21l2	C	G	3: 86,546,989	G235R	probably benign	Het
Mapk8	T	C	14: 33,382,208	E417G	probably benign	Het
Mapk8ip3	G	A	17: 24,909,171		probably benign	Het
Mettl1	A	G	10: 127,045,077	T203A	probably benign	Het
Mettl9	T	C	7: 121,076,313	V312A	probably damaging	Het
Mex3d	A	G	10: 80,386,894	V176A	probably benign	Het
Mmp3	T	C	9: 7,449,790	S225P	probably damaging	Het
Mrvi1	G	A	7: 110,876,897	P757S	probably benign	Het
Neb	G	A	2: 52,188,677		probably benign	Het
Ninj2	C	T	6: 120,198,051	A51V	possibly damaging	Het
Nle1	A	G	11: 82,905,379		probably benign	Het
Nol9	T	C	4: 152,052,605	Y532H	probably benign	Het
Nr2c1	T	A	10: 94,171,158	V286E	probably benign	Het
Olfr1183	T	G	2: 88,461,925	L195R	probably damaging	Het
Olfr1272	A	T	2: 90,282,404	M57K	probably damaging	Het
Olfr308	T	C	7: 86,321,292	Y220C	probably benign	Het
Olfr481	T	A	7: 108,080,872	I26N	possibly damaging	Het
Olfr670	T	A	7: 104,959,943	H263L	probably damaging	Het
Olfr816	A	G	10: 129,911,916	Y121H	probably benign	Het
Olfr827	A	G	10: 130,210,620	L170P	probably damaging	Het
Ovch2	A	T	7: 107,801,136	V15D	probably damaging	Het
Pclo	T	G	5: 14,681,734	S3417A	unknown	Het
Pet2	C	A	X: 89,405,209	R438L	probably benign	Het
Pex1	T	A	5: 3,633,759	M1085K	probably damaging	Het
Plscr2	T	C	9: 92,282,135	S6P	probably benign	Het
Pogz	C	T	3: 94,877,025	P722S	possibly damaging	Het
Pom121l2	A	T	13: 21,982,225	D222V	probably benign	Het
Prpf40a	T	C	2: 53,159,313	Y179C	probably damaging	Het
R3hdm2	A	G	10: 127,458,173	I179V	possibly damaging	Het
Ranbp9	A	C	13: 43,422,658	V355G	probably damaging	Het
Rims2	T	C	15: 39,509,632		probably benign	Het
Ryr2	A	T	13: 11,705,684	S2693T	probably benign	Het
Sbno1	G	A	5: 124,410,285	T111I	probably damaging	Het
Sdk1	A	C	5: 142,046,161	N997T	possibly damaging	Het
Setx	G	T	2: 29,166,289	E39*	probably null	Het
Skint7	T	A	4: 111,980,362	N112K	probably damaging	Het
Slc35e1	T	C	8: 72,492,571		probably benign	Het
Slc4a10	A	T	2: 62,190,848	D80V	probably benign	Het
Susd2	C	A	10: 75,638,603		probably benign	Het
Tcam1	G	A	11: 106,284,078	E120K	probably benign	Het
Tdpoz3	T	C	3: 93,826,365	Y116H	probably benign	Het
Tex26	C	A	5: 149,460,858	D164E	probably benign	Het
Thoc5	G	A	11: 4,902,213		probably benign	Het
Tiparp	A	G	3: 65,531,436	R58G	probably benign	Het
Trim66	A	T	7: 109,475,264	C597S	probably damaging	Het
Ugt2a3	T	A	5: 87,336,490	Q225L	probably benign	Het
Vmn1r25	T	A	6: 57,978,711	I198L	probably benign	Het
Vmn2r106	A	T	17: 20,279,019	V210D	possibly damaging	Het
Vmn2r124	T	C	17: 18,064,145	F483L	probably damaging	Het
Vmn2r78	A	G	7: 86,921,311	K346E	probably benign	Het
Zfhx4	T	A	3: 5,401,161	S2126R	possibly damaging	Het
Zfp608	C	T	18: 54,898,994	G625R	probably benign	Het
Zkscan5	A	G	5: 145,212,575	D234G	probably damaging	Het
Zscan10	T	A	17: 23,605,915	V115E	probably damaging	Het

Other mutations in Tcf3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01798:Tcf3	APN	10	80413209	missense	probably benign	0.30
IGL02676:Tcf3	APN	10	80421091	missense	probably damaging	1.00
IGL03066:Tcf3	APN	10	80413045	missense	probably damaging	0.97
R0165:Tcf3	UTSW	10	80412997	missense	probably damaging	1.00
R0624:Tcf3	UTSW	10	80413334	missense	probably damaging	1.00
R2114:Tcf3	UTSW	10	80410206	missense	probably damaging	1.00
R5034:Tcf3	UTSW	10	80417543	missense	possibly damaging	0.46
R5144:Tcf3	UTSW	10	80415237	missense	probably damaging	0.98
R5347:Tcf3	UTSW	10	80410211	missense	probably damaging	1.00
R5418:Tcf3	UTSW	10	80427683	missense	probably damaging	1.00
R5771:Tcf3	UTSW	10	80421616	intron	probably benign
R5786:Tcf3	UTSW	10	80419499	missense	probably benign	0.06
R5941:Tcf3	UTSW	10	80413044	missense	probably benign	0.06
R6857:Tcf3	UTSW	10	80416899	splice site	probably null
R6982:Tcf3	UTSW	10	80417550	missense	probably damaging	1.00
R7178:Tcf3	UTSW	10	80421599	missense	unknown
R7840:Tcf3	UTSW	10	80410467	missense	possibly damaging	0.87
R8336:Tcf3	UTSW	10	80421166	missense	probably benign
R8958:Tcf3	UTSW	10	80410257	missense	probably damaging	1.00
R9090:Tcf3	UTSW	10	80417357	missense	probably benign	0.28
R9271:Tcf3	UTSW	10	80417357	missense	probably benign	0.28
R9429:Tcf3	UTSW	10	80416602	missense	probably benign	0.00
X0022:Tcf3	UTSW	10	80417458	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGGCTAACGAGCACCTCTCATGAC -3'
(R):5'- CAGCAGTGACCAGAACAGTTCTTCC -3'

Sequencing Primer
(F):5'- TAGCATCCGACTCACTGCC -3'
(R):5'- TTTGACCCTAGCCGGGTAAG -3'

Posted On

2013-05-23