Mutagenetix > Incidental Mutation

Incidental Mutation 'R4952:Gtf2a1'

382086

Institutional Source

Beutler Lab

Gene Symbol

Gtf2a1

Ensembl Gene

ENSMUSG00000020962

Gene Name

general transcription factor II A, 1

Synonyms

37kDa, 6330549H03Rik, Tfiia1, TfIIAa/b, 19kDa

MMRRC Submission

042549-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4952 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

91522036-91557261 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 91542523 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 59 (F59L)

Ref Sequence

ENSEMBL: ENSMUSP00000021345 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021345] [ENSMUST00000063314]

AlphaFold

Q99PM3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000021345
AA Change: F59L

PolyPhen 2 Score 0.702 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000021345
Gene: ENSMUSG00000020962
AA Change: F59L

Domain	Start	End	E-Value	Type
TFIIA	12	378	5.47e-146	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000063314
AA Change: F20L

PolyPhen 2 Score 0.301 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000068562
Gene: ENSMUSG00000020962
AA Change: F20L

Domain	Start	End	E-Value	Type
Pfam:TFIIA	1	339	9.3e-68	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000116715

Meta Mutation Damage Score

0.1558

Coding Region Coverage

1x: 99.0%
3x: 98.3%
10x: 96.5%
20x: 93.0%

Validation Efficiency

99% (93/94)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Accurate transcription initiation on TATA-containing class II genes involves the ordered assembly of RNA polymerase II (POLR2A; MIM 180660) and several general initiation factors (summarized by DeJong and Roeder, 1993 [PubMed 8224848]). One of these factors is TFIIA, which when purified from HeLa extracts consists of 35-, 19-, and 12-kD subunits.[supplied by OMIM, Jul 2010]
PHENOTYPE: Mice homozygous for a hypomorphic allele where D/G cleavage residues are replaced with noncleavable A/A show neonatal lethality, feeding defects, low testis weight, and male infertility associated with azoospermia, small seminiferous tubules, lack of elongating spermatids, and increased apoptosis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522L14Rik	A	G	5: 109,887,063 (GRCm39)		probably null	Het
4933421I07Rik	T	C	7: 42,097,083 (GRCm39)	Y76C	possibly damaging	Het
Adcy4	C	T	14: 56,016,486 (GRCm39)	D322N	probably damaging	Het
Ak9	A	G	10: 41,296,585 (GRCm39)	M1444V	probably benign	Het
Amfr	A	G	8: 94,699,787 (GRCm39)		probably benign	Het
Ankef1	A	G	2: 136,392,449 (GRCm39)	E546G	probably damaging	Het
Ankrd24	A	G	10: 81,482,982 (GRCm39)	M977V	probably benign	Het
Ap3m1	A	T	14: 21,090,134 (GRCm39)	S5T	probably benign	Het
Aqr	C	A	2: 113,940,418 (GRCm39)	D1243Y	probably damaging	Het
Arhgef2	T	C	3: 88,549,769 (GRCm39)	L591P	probably damaging	Het
Arid4a	C	A	12: 71,070,299 (GRCm39)	T70K	possibly damaging	Het
Asphd1	C	T	7: 126,547,857 (GRCm39)	A149T	probably benign	Het
Avpr1a	T	A	10: 122,285,659 (GRCm39)	M317K	probably damaging	Het
Birc2	T	C	9: 7,836,741 (GRCm39)	I109V	probably damaging	Het
Catsperd	A	G	17: 56,939,303 (GRCm39)	Y44C	probably damaging	Het
Crygb	T	G	1: 65,121,268 (GRCm39)	S20R	probably benign	Het
Cyp3a25	T	C	5: 145,928,334 (GRCm39)	N237S	probably benign	Het
Dkk3	C	T	7: 111,717,558 (GRCm39)	A304T	probably benign	Het
Dst	T	C	1: 34,310,503 (GRCm39)	L4101S	probably damaging	Het
Dysf	A	G	6: 84,126,968 (GRCm39)	N1407S	possibly damaging	Het
Epb41	A	G	4: 131,727,581 (GRCm39)	V265A	probably damaging	Het
Faim2	C	T	15: 99,419,109 (GRCm39)	E75K	possibly damaging	Het
Fam237b	T	A	5: 5,625,387 (GRCm39)	F28I	probably benign	Het
Fbn1	T	A	2: 125,159,454 (GRCm39)	D2208V	probably damaging	Het
Fbxo28	A	G	1: 182,153,950 (GRCm39)	S129P	probably damaging	Het
Fbxw14	T	A	9: 109,105,269 (GRCm39)	I299L	probably benign	Het
Fras1	C	T	5: 96,795,357 (GRCm39)	A1050V	probably benign	Het
Fyb1	C	A	15: 6,668,292 (GRCm39)	T495K	probably damaging	Het
Ghdc	A	T	11: 100,659,977 (GRCm39)	W257R	probably damaging	Het
Gm10719	T	C	9: 3,018,962 (GRCm39)	L69S	probably benign	Het
Gm12250	G	T	11: 58,079,210 (GRCm39)		noncoding transcript	Het
Gm4846	A	T	1: 166,311,503 (GRCm39)	F452Y	probably damaging	Het
Gpbp1	T	C	13: 111,577,284 (GRCm39)	D202G	probably damaging	Het
Gpd2	C	A	2: 57,197,025 (GRCm39)	Y193*	probably null	Het
Grhl2	G	T	15: 37,287,493 (GRCm39)	R229L	probably benign	Het
Heatr1	G	T	13: 12,425,480 (GRCm39)	W640L	probably benign	Het
Kalrn	A	T	16: 34,177,785 (GRCm39)		probably null	Het
Keap1	T	C	9: 21,148,582 (GRCm39)	T142A	probably damaging	Het
Kpna2	G	A	11: 106,882,061 (GRCm39)	T255M	probably damaging	Het
Kpna3	A	G	14: 61,607,838 (GRCm39)	C456R	probably damaging	Het
Lama1	G	A	17: 68,074,561 (GRCm39)		probably null	Het
Lrrc37	T	C	11: 103,505,033 (GRCm39)	T2312A	possibly damaging	Het
Mag	C	A	7: 30,608,581 (GRCm39)	E178*	probably null	Het
Map3k13	A	G	16: 21,729,769 (GRCm39)	I467V	probably benign	Het
Mga	A	G	2: 119,733,782 (GRCm39)	E210G	probably damaging	Het
Msi2	C	T	11: 88,257,610 (GRCm39)		probably null	Het
Naa16	A	T	14: 79,582,525 (GRCm39)	D521E	probably damaging	Het
Nav2	C	T	7: 48,954,288 (GRCm39)		probably benign	Het
Nek10	T	A	14: 14,860,986 (GRCm38)	L513M	possibly damaging	Het
Nek5	T	C	8: 22,586,815 (GRCm39)	K332R	probably benign	Het
Nek5	T	A	8: 22,569,104 (GRCm39)	I573L	probably benign	Het
Ntn1	CCTTCTTCT	CCTTCT	11: 68,103,852 (GRCm39)		probably benign	Het
Odad1	A	C	7: 45,591,615 (GRCm39)	E293A	probably damaging	Het
Or2w1	G	A	13: 21,317,514 (GRCm39)	V190I	probably benign	Het
Or5v1b	A	T	17: 37,841,641 (GRCm39)	T258S	possibly damaging	Het
Or6c204	T	A	10: 129,022,466 (GRCm39)	T275S	probably benign	Het
Or8b12b	T	A	9: 37,684,360 (GRCm39)	M135K	probably damaging	Het
Orai1	T	G	5: 123,167,313 (GRCm39)	V162G	probably damaging	Het
P2rx6	T	C	16: 17,385,308 (GRCm39)	S134P	probably damaging	Het
Pappa2	G	A	1: 158,684,706 (GRCm39)	T811I	probably null	Het
Pcdhga10	T	C	18: 37,880,213 (GRCm39)		probably benign	Het
Pex16	C	T	2: 92,209,405 (GRCm39)	R241*	probably null	Het
Plxnb1	T	C	9: 108,943,904 (GRCm39)	F1969L	probably damaging	Het
Postn	A	G	3: 54,297,736 (GRCm39)		probably benign	Het
Prdm15	A	T	16: 97,607,277 (GRCm39)	I752N	probably damaging	Het
Rasgef1c	A	T	11: 49,870,339 (GRCm39)	K468M	probably damaging	Het
Rbfox1	A	G	16: 7,094,952 (GRCm39)	S111G	probably benign	Het
Rbm28	T	C	6: 29,138,597 (GRCm39)	D405G	probably damaging	Het
Rell1	A	G	5: 64,097,010 (GRCm39)		probably benign	Het
Rfx3	A	G	19: 27,808,072 (GRCm39)	S224P	probably damaging	Het
Scarb2	A	T	5: 92,602,636 (GRCm39)	I260K	probably damaging	Het
Septin4	A	G	11: 87,458,598 (GRCm39)	N324S	probably benign	Het
Slc15a4	A	G	5: 127,680,901 (GRCm39)	F72L	probably damaging	Het
Spg7	C	A	8: 123,816,910 (GRCm39)	R534S	probably damaging	Het
Stoml2	T	C	4: 43,029,589 (GRCm39)	T164A	probably benign	Het
Syt11	C	T	3: 88,669,590 (GRCm39)	G101S	possibly damaging	Het
Traj12	A	G	14: 54,444,013 (GRCm39)		probably benign	Het
Traj7	A	T	14: 54,448,981 (GRCm39)		probably benign	Het
Tysnd1	C	T	10: 61,537,855 (GRCm39)	T175I	possibly damaging	Het
Usp48	T	G	4: 137,334,004 (GRCm39)	Y139*	probably null	Het
Vmn2r72	A	G	7: 85,400,317 (GRCm39)	L244P	probably benign	Het
Wasf1	C	A	10: 40,812,186 (GRCm39)	P325Q	unknown	Het
Zc3h18	T	A	8: 123,137,639 (GRCm39)		probably benign	Het
Zfp712	A	G	13: 67,188,905 (GRCm39)	S541P	possibly damaging	Het

Other mutations in Gtf2a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01510:Gtf2a1	APN	12	91,534,607 (GRCm39)	missense	probably benign	0.00
IGL02561:Gtf2a1	APN	12	91,542,527 (GRCm39)	missense	possibly damaging	0.93
IGL03035:Gtf2a1	APN	12	91,539,411 (GRCm39)	splice site	probably benign
PIT4618001:Gtf2a1	UTSW	12	91,534,543 (GRCm39)	missense	probably benign	0.09
R0436:Gtf2a1	UTSW	12	91,535,047 (GRCm39)	splice site	probably null
R1595:Gtf2a1	UTSW	12	91,556,323 (GRCm39)	missense	probably damaging	0.98
R2240:Gtf2a1	UTSW	12	91,553,513 (GRCm39)	missense	possibly damaging	0.87
R4020:Gtf2a1	UTSW	12	91,539,351 (GRCm39)	missense	possibly damaging	0.92
R4043:Gtf2a1	UTSW	12	91,542,441 (GRCm39)	missense	probably benign	0.00
R4044:Gtf2a1	UTSW	12	91,542,441 (GRCm39)	missense	probably benign	0.00
R4095:Gtf2a1	UTSW	12	91,542,411 (GRCm39)	missense	possibly damaging	0.68
R4584:Gtf2a1	UTSW	12	91,529,700 (GRCm39)	missense	possibly damaging	0.66
R4585:Gtf2a1	UTSW	12	91,529,700 (GRCm39)	missense	possibly damaging	0.66
R5465:Gtf2a1	UTSW	12	91,534,565 (GRCm39)	missense	possibly damaging	0.86
R5566:Gtf2a1	UTSW	12	91,534,368 (GRCm39)	missense	possibly damaging	0.63
R7055:Gtf2a1	UTSW	12	91,553,523 (GRCm39)	missense	possibly damaging	0.93
R7220:Gtf2a1	UTSW	12	91,534,498 (GRCm39)	missense	probably benign	0.00
R7282:Gtf2a1	UTSW	12	91,534,609 (GRCm39)	missense	possibly damaging	0.56
R7459:Gtf2a1	UTSW	12	91,542,426 (GRCm39)	missense	probably benign	0.00
R7484:Gtf2a1	UTSW	12	91,529,747 (GRCm39)	missense	probably benign	0.01
R9292:Gtf2a1	UTSW	12	91,534,964 (GRCm39)	nonsense	probably null
R9372:Gtf2a1	UTSW	12	91,534,592 (GRCm39)	missense	probably damaging	1.00
X0063:Gtf2a1	UTSW	12	91,539,386 (GRCm39)	missense	possibly damaging	0.91

Predicted Primers

PCR Primer
(F):5'- CTTGTAAGGCACAACAGGGAC -3'
(R):5'- GGAACCCTGTTAAATAATACCTGC -3'

Sequencing Primer
(F):5'- AGGGACCTCCAGCCTTCTC -3'
(R):5'- GAAGCTTTACTGTTCTTCGTC -3'

Posted On

2016-04-27