Mutagenetix > Incidental Mutation

Incidental Mutation 'R5418:Tcf3'

427864

Institutional Source

Beutler Lab

Gene Symbol

Tcf3

Ensembl Gene

ENSMUSG00000020167

Gene Name

transcription factor 3

Synonyms

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

MMRRC Submission

042986-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.956) question?

Stock #

R5418 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

80245348-80269481 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 80263517 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 46 (F46L)

Ref Sequence

ENSEMBL: ENSMUSP00000100978 (fasta)

Gene Model

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

AlphaFold

P15806

Predicted Effect

probably damaging
Transcript: ENSMUST00000020377
AA Change: F46L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000020377
Gene: ENSMUSG00000020167
AA Change: F46L

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

probably damaging
Transcript: ENSMUST00000020379
AA Change: F46L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000020379
Gene: ENSMUSG00000020167
AA Change: F46L

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

probably damaging
Transcript: ENSMUST00000105339
AA Change: F46L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000100976
Gene: ENSMUSG00000020167
AA Change: F46L

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: F46L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100977
Gene: ENSMUSG00000020167
AA Change: F46L

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

probably damaging
Transcript: ENSMUST00000105341
AA Change: F46L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000100978
Gene: ENSMUSG00000020167
AA Change: F46L

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

probably damaging
Transcript: ENSMUST00000105342
AA Change: F46L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100979
Gene: ENSMUSG00000020167
AA Change: F46L

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: F46L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100980
Gene: ENSMUSG00000020167
AA Change: F46L

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: F46L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100981
Gene: ENSMUSG00000020167
AA Change: F46L

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

probably damaging
Transcript: ENSMUST00000105345
AA Change: F46L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100982
Gene: ENSMUSG00000020167
AA Change: F46L

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

probably damaging
Transcript: ENSMUST00000105346
AA Change: F46L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100983
Gene: ENSMUSG00000020167
AA Change: F46L

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

unknown
Transcript: ENSMUST00000156990
AA Change: F37L

SMART Domains

Protein: ENSMUSP00000121172
Gene: ENSMUSG00000020167
AA Change: F37L

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

0.5073

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

99% (81/82)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930568D16Rik	A	G	2: 35,244,738 (GRCm39)	S205P	probably damaging	Het
Abcc1	T	C	16: 14,278,996 (GRCm39)	V1102A	probably benign	Het
Acad8	A	T	9: 26,896,853 (GRCm39)	M202K	probably damaging	Het
Acoxl	T	A	2: 127,719,722 (GRCm39)	M161K	probably benign	Het
Adamts4	T	A	1: 171,080,143 (GRCm39)	V35E	probably damaging	Het
Add2	A	G	6: 86,087,894 (GRCm39)	S614G	probably benign	Het
Adgrv1	T	A	13: 81,567,427 (GRCm39)	I5249L	probably benign	Het
Agps	A	G	2: 75,689,248 (GRCm39)	T252A	probably damaging	Het
Alms1-ps1	G	A	6: 85,732,584 (GRCm39)		noncoding transcript	Het
Ankrd24	T	A	10: 81,480,776 (GRCm39)		probably benign	Het
Bcl9l	A	G	9: 44,416,733 (GRCm39)	Q218R	possibly damaging	Het
Bin2	T	C	15: 100,547,027 (GRCm39)	Y232C	probably damaging	Het
Bptf	A	G	11: 107,002,120 (GRCm39)	Y331H	probably damaging	Het
Ccr10	C	T	11: 101,064,904 (GRCm39)	V209M	probably benign	Het
Cflar	A	T	1: 58,791,810 (GRCm39)	D371V	possibly damaging	Het
Col1a2	A	G	6: 4,516,931 (GRCm39)		probably benign	Het
Crlf2	A	G	5: 109,704,899 (GRCm39)	V104A	probably benign	Het
Dennd1c	CCGCCCCTCGCTGACAGC	CC	17: 57,373,755 (GRCm39)		probably null	Het
Dmxl2	A	G	9: 54,281,935 (GRCm39)		probably null	Het
Dnah17	C	A	11: 117,985,810 (GRCm39)	E1422D	probably benign	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Efcab11	A	G	12: 99,821,877 (GRCm39)	L80S	possibly damaging	Het
Emc8	G	A	8: 121,385,342 (GRCm39)	T130M	probably damaging	Het
Epha6	C	A	16: 60,245,198 (GRCm39)	A334S	possibly damaging	Het
Erc2	A	G	14: 27,688,467 (GRCm39)	M196V	probably benign	Het
Etnk2	T	C	1: 133,300,995 (GRCm39)	I254T	probably damaging	Het
Fam120b	C	T	17: 15,622,061 (GRCm39)	T13M	probably damaging	Het
Fam234b	A	G	6: 135,203,966 (GRCm39)	K423E	probably benign	Het
Fcgbp	G	A	7: 27,784,738 (GRCm39)	G266D	probably damaging	Het
Fndc4	A	T	5: 31,451,978 (GRCm39)	S146R	probably benign	Het
Frmd3	G	A	4: 74,079,935 (GRCm39)		probably null	Het
Glrx2	C	A	1: 143,615,446 (GRCm39)	S16R	possibly damaging	Het
Gm26526	T	G	7: 39,238,358 (GRCm39)		noncoding transcript	Het
Hc	C	T	2: 34,898,195 (GRCm39)		probably null	Het
Herc2	T	C	7: 55,787,313 (GRCm39)	C1695R	probably damaging	Het
Hic1	A	G	11: 75,057,425 (GRCm39)		probably null	Het
Igkv4-92	A	T	6: 68,732,564 (GRCm39)	V5E	possibly damaging	Het
Irs1	G	A	1: 82,266,491 (GRCm39)	T575I	probably damaging	Het
Kcp	A	T	6: 29,504,283 (GRCm39)	Y143*	probably null	Het
Klb	A	G	5: 65,540,813 (GRCm39)	N969D	probably benign	Het
Klra6	T	A	6: 129,990,393 (GRCm39)	L239F	probably damaging	Het
Lhx6	A	G	2: 35,977,378 (GRCm39)		probably null	Het
Lrrc34	G	A	3: 30,696,923 (GRCm39)	P116S	possibly damaging	Het
Map3k9	T	A	12: 81,790,591 (GRCm39)	K321*	probably null	Het
Mapk14	T	C	17: 28,960,817 (GRCm39)	V196A	possibly damaging	Het
Matcap2	G	T	9: 22,343,066 (GRCm39)	R187L	probably damaging	Het
Mmp1b	T	C	9: 7,384,897 (GRCm39)	I251V	possibly damaging	Het
Mtmr12	T	C	15: 12,270,045 (GRCm39)	L711P	probably damaging	Het
Mylk	T	C	16: 34,732,600 (GRCm39)	S627P	probably benign	Het
Nbea	A	T	3: 55,553,410 (GRCm39)	Y2631N	possibly damaging	Het
Ncoa7	A	G	10: 30,524,035 (GRCm39)	V153A	probably damaging	Het
Or4a79	T	C	2: 89,552,343 (GRCm39)	I37M	probably benign	Het
Pax6	A	T	2: 105,521,910 (GRCm39)	D175V	probably benign	Het
Piezo1	A	G	8: 123,213,519 (GRCm39)	L1793P	probably damaging	Het
Pkp4	T	C	2: 59,140,506 (GRCm39)	V404A	probably benign	Het
Plxnb2	A	G	15: 89,050,694 (GRCm39)	Y421H	probably benign	Het
Prkdc	T	G	16: 15,612,961 (GRCm39)	V3173G	probably benign	Het
Prss40	A	T	1: 34,599,840 (GRCm39)	I49N	probably benign	Het
Prx	T	A	7: 27,216,699 (GRCm39)	V400E	probably damaging	Het
Rbm11	A	C	16: 75,393,423 (GRCm39)	T40P	probably damaging	Het
Resf1	T	C	6: 149,227,634 (GRCm39)	Y227H	probably damaging	Het
Scara5	CG	C	14: 65,997,111 (GRCm39)		probably null	Het
Sema3f	A	G	9: 107,569,820 (GRCm39)	Y70H	probably damaging	Het
Senp6	G	A	9: 80,029,151 (GRCm39)	E505K	possibly damaging	Het
Slc25a3	T	C	10: 90,955,398 (GRCm39)	I147M	probably benign	Het
Slc4a7	T	A	14: 14,760,280 (GRCm38)	S572T	probably benign	Het
Smarcal1	C	T	1: 72,638,068 (GRCm39)	P501S	probably benign	Het
Sox7	C	T	14: 64,185,396 (GRCm39)	T144M	probably benign	Het
Taar1	T	C	10: 23,797,214 (GRCm39)	F304S	possibly damaging	Het
Tmem184c	A	G	8: 78,324,449 (GRCm39)	V347A	probably damaging	Het
Tpcn2	C	T	7: 144,832,518 (GRCm39)	E113K	probably damaging	Het
Vmn1r232	T	A	17: 21,134,378 (GRCm39)	Y74F	possibly damaging	Het
Vmn2r102	C	T	17: 19,914,415 (GRCm39)	T660I	probably damaging	Het
Zdhhc3	A	G	9: 122,909,456 (GRCm39)	M234T	probably damaging	Het
Zfp960	T	A	17: 17,307,805 (GRCm39)	L173H	probably damaging	Het

Other mutations in Tcf3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01798:Tcf3	APN	10	80,249,043 (GRCm39)	missense	probably benign	0.30
IGL02676:Tcf3	APN	10	80,256,925 (GRCm39)	missense	probably damaging	1.00
IGL03066:Tcf3	APN	10	80,248,879 (GRCm39)	missense	probably damaging	0.97
R0165:Tcf3	UTSW	10	80,248,831 (GRCm39)	missense	probably damaging	1.00
R0401:Tcf3	UTSW	10	80,256,992 (GRCm39)	missense	probably damaging	0.99
R0624:Tcf3	UTSW	10	80,249,168 (GRCm39)	missense	probably damaging	1.00
R2114:Tcf3	UTSW	10	80,246,040 (GRCm39)	missense	probably damaging	1.00
R5034:Tcf3	UTSW	10	80,253,377 (GRCm39)	missense	possibly damaging	0.46
R5144:Tcf3	UTSW	10	80,251,071 (GRCm39)	missense	probably damaging	0.98
R5347:Tcf3	UTSW	10	80,246,045 (GRCm39)	missense	probably damaging	1.00
R5771:Tcf3	UTSW	10	80,257,450 (GRCm39)	intron	probably benign
R5786:Tcf3	UTSW	10	80,255,333 (GRCm39)	missense	probably benign	0.06
R5941:Tcf3	UTSW	10	80,248,878 (GRCm39)	missense	probably benign	0.06
R6857:Tcf3	UTSW	10	80,252,733 (GRCm39)	splice site	probably null
R6982:Tcf3	UTSW	10	80,253,384 (GRCm39)	missense	probably damaging	1.00
R7178:Tcf3	UTSW	10	80,257,433 (GRCm39)	missense	unknown
R7840:Tcf3	UTSW	10	80,246,301 (GRCm39)	missense	possibly damaging	0.87
R8336:Tcf3	UTSW	10	80,257,000 (GRCm39)	missense	probably benign
R8958:Tcf3	UTSW	10	80,246,091 (GRCm39)	missense	probably damaging	1.00
R9090:Tcf3	UTSW	10	80,253,191 (GRCm39)	missense	probably benign	0.28
R9271:Tcf3	UTSW	10	80,253,191 (GRCm39)	missense	probably benign	0.28
R9429:Tcf3	UTSW	10	80,252,436 (GRCm39)	missense	probably benign	0.00
X0022:Tcf3	UTSW	10	80,253,292 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAGACTGACCGTGGTTATTCC -3'
(R):5'- CAGCTCTGTTCCAGCCTAAC -3'

Sequencing Primer
(F):5'- TTGTTCAAAATCCAATCACCGGGG -3'
(R):5'- ACTCCAGGAAACCTAGTCTTTGGG -3'

Posted On

2016-09-01