Mutagenetix > Incidental Mutation

Incidental Mutation 'R7840:Tcf3'

606228

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

045894-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.956) question?

Stock #

R7840 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

80245348-80269481 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 80246301 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 581 (A581T)

Ref Sequence

ENSEMBL: ENSMUSP00000100981 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020372] [ENSMUST00000020377] [ENSMUST00000020379] [ENSMUST00000105339] [ENSMUST00000105340] [ENSMUST00000105341] [ENSMUST00000105342] [ENSMUST00000105344] [ENSMUST00000105343] [ENSMUST00000105345] [ENSMUST00000105346]

AlphaFold

P15806

Predicted Effect

probably benign
Transcript: ENSMUST00000020372

SMART Domains

Protein: ENSMUSP00000020372
Gene: ENSMUSG00000020163

Domain	Start	End	E-Value	Type
Pfam:UCR_6-4kD	1	55	1.2e-36	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000020377

SMART Domains

Protein: ENSMUSP00000020377
Gene: ENSMUSG00000020167

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: A580T

PolyPhen 2 Score 0.536 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000020379
Gene: ENSMUSG00000020167
AA Change: A580T

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 benign
Transcript: ENSMUST00000105339

SMART Domains

Protein: ENSMUSP00000100976
Gene: ENSMUSG00000020167

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 benign
Transcript: ENSMUST00000105340
AA Change: A579T

PolyPhen 2 Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000100977
Gene: ENSMUSG00000020167
AA Change: A579T

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 benign
Transcript: ENSMUST00000105341
AA Change: A576T

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000100978
Gene: ENSMUSG00000020167
AA Change: A576T

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 benign
Transcript: ENSMUST00000105342

SMART Domains

Protein: ENSMUSP00000100979
Gene: ENSMUSG00000020167

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

possibly damaging
Transcript: ENSMUST00000105344
AA Change: A581T

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000100981
Gene: ENSMUSG00000020167
AA Change: A581T

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 benign
Transcript: ENSMUST00000105343
AA Change: A580T

PolyPhen 2 Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000100980
Gene: ENSMUSG00000020167
AA Change: A580T

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

possibly damaging
Transcript: ENSMUST00000105345
AA Change: A579T

PolyPhen 2 Score 0.751 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000100982
Gene: ENSMUSG00000020167
AA Change: A579T

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 benign
Transcript: ENSMUST00000105346

SMART Domains

Protein: ENSMUSP00000100983
Gene: ENSMUSG00000020167

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

SMART Domains

Protein: ENSMUSP00000121172
Gene: ENSMUSG00000020167
AA Change: A568T

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

0.1114

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (73/74)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca16	A	G	7: 120,074,689 (GRCm39)	N577S	probably benign	Het
Ang4	A	G	14: 52,001,529 (GRCm39)	S140P	probably damaging	Het
Ankdd1b	T	C	13: 96,556,306 (GRCm39)		probably null	Het
Anln	G	T	9: 22,274,019 (GRCm39)	A606D	probably benign	Het
Ano5	T	G	7: 51,237,480 (GRCm39)	V768G	possibly damaging	Het
Ccdc180	A	T	4: 45,900,461 (GRCm39)	Y275F	possibly damaging	Het
Chpf	T	C	1: 75,453,271 (GRCm39)	Y334C	probably damaging	Het
Chrdl2	T	C	7: 99,682,863 (GRCm39)	L381S	probably damaging	Het
Cibar2	T	C	8: 120,893,372 (GRCm39)	D273G	probably benign	Het
Cox20	A	T	1: 178,150,126 (GRCm39)	Y100F	probably benign	Het
Dbn1	T	C	13: 55,623,322 (GRCm39)	D433G	possibly damaging	Het
Dclre1a	A	T	19: 56,519,684 (GRCm39)	I983N	probably damaging	Het
Dok6	A	T	18: 89,578,182 (GRCm39)	H78Q	probably benign	Het
Efcab3	G	A	11: 104,624,539 (GRCm39)	D878N	probably benign	Het
Fpr1	A	T	17: 18,097,634 (GRCm39)	F118L	probably benign	Het
Fscn3	A	G	6: 28,430,175 (GRCm39)	Y115C	probably damaging	Het
Gabra4	A	C	5: 71,798,256 (GRCm39)		probably null	Het
Gm45861	T	C	8: 28,072,751 (GRCm39)	V1290A	unknown	Het
Hivep1	T	C	13: 42,308,828 (GRCm39)	V356A	probably benign	Het
Ikbip	T	C	10: 90,937,617 (GRCm39)	Y97H	possibly damaging	Het
Il10	A	G	1: 130,947,805 (GRCm39)	T53A	probably benign	Het
Inpp5f	T	C	7: 128,296,526 (GRCm39)	V959A	probably benign	Het
Insr	T	C	8: 3,308,415 (GRCm39)	E207G	probably benign	Het
Kndc1	T	A	7: 139,503,731 (GRCm39)	S1012T	probably damaging	Het
Krtap5-1	ACAGGGCTTGCAGCAGCTGGACTGACAGCAGCAGGGCTTGCAGCAGCTGGACTGACAGCAGCAGGGCTTGCAGCAGCTGGACTGACAGCAG	ACAGGGCTTGCAGCAGCTGGACTGACAGCAGCAGGGCTTGCAGCAGCTGGACTGACAGCAG	7: 141,850,333 (GRCm39)		probably benign	Het
Ksr2	T	C	5: 117,693,329 (GRCm39)	V259A	probably benign	Het
Lox	A	T	18: 52,658,194 (GRCm39)	Y326*	probably null	Het
Lpin2	C	A	17: 71,537,269 (GRCm39)	T272N	probably benign	Het
Lrp2	C	T	2: 69,295,128 (GRCm39)	E3397K	probably damaging	Het
Megf11	G	A	9: 64,602,709 (GRCm39)	C850Y	possibly damaging	Het
Morc1	T	C	16: 48,319,147 (GRCm39)	F284L	probably benign	Het
Moxd2	T	A	6: 40,862,378 (GRCm39)	D147V	possibly damaging	Het
Mrpl21	T	C	19: 3,337,752 (GRCm39)	L153P	probably damaging	Het
Naip2	T	C	13: 100,280,917 (GRCm39)	T1432A	probably benign	Het
Naip6	T	A	13: 100,451,979 (GRCm39)	D211V	probably damaging	Het
Ncoa5	T	C	2: 164,854,816 (GRCm39)	H102R	possibly damaging	Het
Ndel1	A	T	11: 68,720,806 (GRCm39)	C293*	probably null	Het
Ninl	A	T	2: 150,808,016 (GRCm39)	M82K	probably benign	Het
Nrcam	G	A	12: 44,587,858 (GRCm39)		probably null	Het
Nup210l	A	T	3: 90,030,036 (GRCm39)	I250L	probably benign	Het
Obscn	T	C	11: 58,968,776 (GRCm39)	E2532G	possibly damaging	Het
Or1e1	C	A	11: 73,244,585 (GRCm39)	A2E	probably benign	Het
Or5v1	G	T	17: 37,809,868 (GRCm39)	G109C	probably damaging	Het
Or8j3c	A	G	2: 86,253,583 (GRCm39)	F146L	probably benign	Het
Osgin1	G	A	8: 120,171,773 (GRCm39)	S189N	possibly damaging	Het
Otud7b	A	G	3: 96,062,690 (GRCm39)	E643G	probably damaging	Het
Phldb2	T	A	16: 45,571,727 (GRCm39)	T1222S	probably damaging	Het
Pwp1	C	T	10: 85,723,914 (GRCm39)	R472W	probably damaging	Het
Rad21	T	C	15: 51,836,538 (GRCm39)	Y211C	probably damaging	Het
Rexo1	A	G	10: 80,386,572 (GRCm39)	V162A	probably benign	Het
Rtl1	C	T	12: 109,560,589 (GRCm39)	V417I	probably benign	Het
Setbp1	G	A	18: 78,826,639 (GRCm39)	P1325S	probably benign	Het
Shld1	A	G	2: 132,592,510 (GRCm39)	T186A	probably damaging	Het
Shld2	A	G	14: 33,959,523 (GRCm39)	Y820H	probably damaging	Het
Skint7	G	T	4: 111,839,423 (GRCm39)	C239F	probably benign	Het
Slc25a1	A	G	16: 17,744,138 (GRCm39)	L221P	probably benign	Het
Snrnp70	T	A	7: 45,026,214 (GRCm39)	D385V	unknown	Het
Sp7	A	C	15: 102,267,533 (GRCm39)	V109G	probably benign	Het
Syne1	A	T	10: 5,082,078 (GRCm39)	Y849N	probably damaging	Het
Tas2r108	T	C	6: 40,470,790 (GRCm39)	F89L	possibly damaging	Het
Tcta	A	G	9: 108,182,986 (GRCm39)	L53P	probably damaging	Het
Traf3ip2	C	G	10: 39,502,451 (GRCm39)	Q200E	probably damaging	Het
Trgc1	A	T	13: 19,400,691 (GRCm39)	Y140F		Het
Tyk2	A	T	9: 21,036,263 (GRCm39)	C75S	probably damaging	Het
Ugt3a1	G	A	15: 9,311,903 (GRCm39)	G382R	probably damaging	Het
Upp2	G	T	2: 58,664,127 (GRCm39)		probably null	Het
Vmn1r212	A	T	13: 23,067,323 (GRCm39)	F337I	unknown	Het
Vmn1r58	T	C	7: 5,414,242 (GRCm39)		probably benign	Het
Vps13d	A	T	4: 144,830,246 (GRCm39)	V2856D		Het
Wdr37	A	C	13: 8,886,911 (GRCm39)	L292R	probably damaging	Het
Yipf3	T	C	17: 46,561,790 (GRCm39)	I199T	probably benign	Het
Zdhhc23	A	G	16: 43,791,907 (GRCm39)	S289P	possibly damaging	Het
Zfp229	A	T	17: 21,965,131 (GRCm39)	K454*	probably null	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
R5418:Tcf3	UTSW	10	80,263,517 (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
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'- AAGAAGCTGTGACGGCTCAC -3'
(R):5'- GTGACCCAGCAGTACAGATG -3'

Sequencing Primer
(F):5'- TCCGCTTCAAGCAGGCTG -3'
(R):5'- CAGTACAGATGAGGTGCTGTCC -3'

Posted On

2019-12-20