Mutagenetix > Incidental Mutation

Incidental Mutation 'R6246:Gtf2a1l'

505820

Institutional Source

Beutler Lab

Gene Symbol

Gtf2a1l

Ensembl Gene

ENSMUSG00000024154

Gene Name

general transcription factor IIA, 1-like

Synonyms

Gtf2a1lf, 1700011N16Rik, Alf

MMRRC Submission

044436-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.650) question?

Stock #

R6246 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

88976088-89022580 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 88978975 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 58 (R58G)

Ref Sequence

ENSEMBL: ENSMUSP00000024970 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000024970] [ENSMUST00000161481]

AlphaFold

Q8R4I4

Predicted Effect

probably benign
Transcript: ENSMUST00000024970
AA Change: R58G

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000024970
Gene: ENSMUSG00000024154
AA Change: R58G

Domain	Start	End	E-Value	Type
TFIIA	9	468	6.87e-202	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000161481
AA Change: R58G

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000124286
Gene: ENSMUSG00000024154
AA Change: R58G

Domain	Start	End	E-Value	Type
Pfam:TFIIA	9	76	3.2e-29	PFAM
Pfam:TFIIA	70	243	3e-13	PFAM

Meta Mutation Damage Score

0.1661

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.6%

Validation Efficiency

100% (78/78)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The assembly and stability of the RNA polymerase II transcription pre-initiation complex on a eukaryotic core promoter involve the effects of transcription factor IIA (TFIIA) on the interaction between TATA-binding protein (TBP) and DNA. This gene encodes a germ cell-specific counterpart of the large (alpha/beta) subunit of general transcription factor TFIIA that is able to stabilize the binding of TBP to DNA and may be uniquely important to testis biology. Alternative splicing for this locus has been observed and two variants, encoding distinct isoforms, have been identified. Co-transcription of this gene and the neighboring upstream gene generates a rare transcript (SALF), which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Mar 2014]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca7	T	A	10: 79,850,999 (GRCm39)	V2110E	probably damaging	Het
Acaca	C	A	11: 84,206,796 (GRCm39)	T1552K	probably benign	Het
Aknad1	A	G	3: 108,659,148 (GRCm39)	D54G	probably damaging	Het
Ano1	T	C	7: 144,187,462 (GRCm39)	T435A	possibly damaging	Het
Azgp1	A	G	5: 137,983,475 (GRCm39)	D50G	possibly damaging	Het
Bbx	A	G	16: 50,045,023 (GRCm39)	S513P	probably benign	Het
Ccdc85a	C	T	11: 28,526,897 (GRCm39)	S209N	probably damaging	Het
Cdca2	T	A	14: 67,915,277 (GRCm39)	R661*	probably null	Het
Cdhr2	T	C	13: 54,867,523 (GRCm39)	V451A	probably damaging	Het
Cenpt	C	T	8: 106,575,891 (GRCm39)	G152S	possibly damaging	Het
Chd9	A	G	8: 91,659,045 (GRCm39)	T2A	probably damaging	Het
Chst14	G	A	2: 118,757,482 (GRCm39)	C117Y	probably damaging	Het
Cic	C	T	7: 24,971,067 (GRCm39)	T266M	probably damaging	Het
Clec12a	A	T	6: 129,330,733 (GRCm39)	N105I	possibly damaging	Het
Cmah	G	A	13: 24,650,773 (GRCm39)	V525M	probably damaging	Het
Cplane1	T	A	15: 8,239,498 (GRCm39)	L1233H	probably damaging	Het
Cpt1a	T	C	19: 3,426,550 (GRCm39)	L572P	probably damaging	Het
Crybg2	T	C	4: 133,816,657 (GRCm39)	L1365P	probably damaging	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Dlg1	G	A	16: 31,484,468 (GRCm39)	S32N	probably benign	Het
Dnah14	T	C	1: 181,508,453 (GRCm39)	I1877T	probably benign	Het
Duox1	G	T	2: 122,157,655 (GRCm39)	G594C	probably damaging	Het
Eci2	T	C	13: 35,174,181 (GRCm39)	N127D	probably damaging	Het
Ecpas	A	G	4: 58,811,365 (GRCm39)		probably null	Het
Fat4	T	C	3: 38,945,870 (GRCm39)	S1588P	probably damaging	Het
Fer1l4	T	A	2: 155,866,902 (GRCm39)	I1489F	probably damaging	Het
Flrt3	A	G	2: 140,501,721 (GRCm39)	Y636H	probably damaging	Het
Frmd5	T	A	2: 121,381,529 (GRCm39)	H62L	possibly damaging	Het
Gm6309	A	T	5: 146,107,050 (GRCm39)	Y99N	probably damaging	Het
Gm8225	T	C	17: 26,762,652 (GRCm39)	V281A	probably benign	Het
Grep1	C	A	17: 23,929,465 (GRCm39)	G315*	probably null	Het
Grsf1	A	G	5: 88,810,451 (GRCm39)	L353P	possibly damaging	Het
Guf1	G	A	5: 69,715,898 (GRCm39)	G113R	probably damaging	Het
Hfe	A	T	13: 23,892,212 (GRCm39)	F51I	probably damaging	Het
Hibch	T	C	1: 52,943,801 (GRCm39)	S250P	probably damaging	Het
Il1rap	T	A	16: 26,533,631 (GRCm39)	M509K	probably benign	Het
Il4ra	T	C	7: 125,175,577 (GRCm39)	V595A	probably benign	Het
Ints11	A	G	4: 155,972,546 (GRCm39)	T460A	probably benign	Het
Itprid1	A	T	6: 55,944,657 (GRCm39)	K459N	probably damaging	Het
Kdm5a	G	A	6: 120,408,871 (GRCm39)	G1518E	probably damaging	Het
Khsrp	T	C	17: 57,332,324 (GRCm39)	D289G	possibly damaging	Het
Kif14	C	T	1: 136,404,162 (GRCm39)	Q29*	probably null	Het
Krt72	T	C	15: 101,689,372 (GRCm39)	K320R	probably damaging	Het
Lcmt2	A	G	2: 120,970,870 (GRCm39)	L71P	probably damaging	Het
Lmo7	A	T	14: 102,156,136 (GRCm39)	D1037V	probably damaging	Het
Lpo	T	C	11: 87,713,058 (GRCm39)	T15A	unknown	Het
Mia3	G	T	1: 183,126,720 (GRCm39)	T7N	probably damaging	Het
Muc16	A	T	9: 18,488,363 (GRCm39)		probably null	Het
Mup9	T	A	4: 60,375,809 (GRCm39)	Y29F	probably damaging	Het
Nisch	T	C	14: 30,894,516 (GRCm39)	D1105G	probably damaging	Het
Odad1	A	G	7: 45,585,788 (GRCm39)	I116V	probably damaging	Het
Oip5	T	C	2: 119,446,101 (GRCm39)	T136A	probably benign	Het
Or2a52	G	A	6: 43,144,436 (GRCm39)		probably null	Het
Osbpl10	C	A	9: 115,055,842 (GRCm39)	N532K	probably benign	Het
P2ry12	C	T	3: 59,124,950 (GRCm39)	V242I	probably benign	Het
Pdhx	A	T	2: 102,877,137 (GRCm39)	C26S	probably damaging	Het
Pgk2	A	T	17: 40,518,315 (GRCm39)	I371K	probably damaging	Het
Phyhip	T	C	14: 70,704,495 (GRCm39)	V238A	probably damaging	Het
Pla2g4a	G	A	1: 149,748,338 (GRCm39)	T282I	probably damaging	Het
Pld5	A	T	1: 175,791,475 (GRCm39)	C448*	probably null	Het
Plk1	T	A	7: 121,768,659 (GRCm39)	I553N	probably damaging	Het
Ppp1r13l	T	A	7: 19,103,783 (GRCm39)	I88K	probably benign	Het
Rad54l2	A	G	9: 106,577,692 (GRCm39)		probably null	Het
Septin7	A	G	9: 25,218,817 (GRCm39)	E428G	probably benign	Het
Serpina3j	G	A	12: 104,283,706 (GRCm39)	G268D	probably damaging	Het
Smc2	A	T	4: 52,460,289 (GRCm39)	D555V	probably damaging	Het
Spag16	A	T	1: 69,962,980 (GRCm39)	I376F	probably benign	Het
Spag6	G	A	2: 18,703,906 (GRCm39)		probably null	Het
Tecta	T	C	9: 42,289,204 (GRCm39)	I454V	probably benign	Het
Tlcd3b	T	A	7: 126,426,668 (GRCm39)	F30L	probably damaging	Het
Tm9sf1	C	T	14: 55,873,827 (GRCm39)	R557H	probably damaging	Het
Traf5	C	T	1: 191,754,853 (GRCm39)	E28K	probably damaging	Het
Trav23	G	A	14: 54,214,885 (GRCm39)	E33K	probably damaging	Het
Trim32	T	C	4: 65,532,801 (GRCm39)	S453P	probably damaging	Het
Tssk1	A	G	16: 17,713,303 (GRCm39)	T363A	probably benign	Het
Txnrd3	A	G	6: 89,628,523 (GRCm39)	N88S	probably benign	Het
Unc13b	A	G	4: 43,216,246 (GRCm39)	S182G	probably benign	Het
Vmn2r89	A	T	14: 51,693,503 (GRCm39)	R284S	probably damaging	Het
Zbtb14	A	G	17: 69,694,478 (GRCm39)	T59A	possibly damaging	Het
Zcchc2	T	A	1: 105,957,796 (GRCm39)	S756T	possibly damaging	Het
Zfp709	TCGACG	TCG	8: 72,644,552 (GRCm39)		probably benign	Het

Other mutations in Gtf2a1l

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00565:Gtf2a1l	APN	17	89,001,723 (GRCm39)	missense	probably damaging	1.00
IGL00928:Gtf2a1l	APN	17	89,001,890 (GRCm39)	missense	probably benign	0.09
IGL00974:Gtf2a1l	APN	17	89,022,377 (GRCm39)	missense	probably damaging	1.00
IGL01024:Gtf2a1l	APN	17	88,978,719 (GRCm39)	missense	probably damaging	1.00
IGL02429:Gtf2a1l	APN	17	88,976,141 (GRCm39)	start codon destroyed	probably null	0.61
IGL02658:Gtf2a1l	APN	17	88,976,146 (GRCm39)	missense	probably benign	0.01
IGL03377:Gtf2a1l	APN	17	89,019,021 (GRCm39)	missense	probably benign	0.03
R0848:Gtf2a1l	UTSW	17	89,001,657 (GRCm39)	missense	probably damaging	0.99
R0899:Gtf2a1l	UTSW	17	88,976,152 (GRCm39)	missense
R1435:Gtf2a1l	UTSW	17	89,001,743 (GRCm39)	missense	probably damaging	1.00
R1716:Gtf2a1l	UTSW	17	89,002,008 (GRCm39)	missense	probably benign	0.06
R1861:Gtf2a1l	UTSW	17	89,022,382 (GRCm39)	missense	probably damaging	1.00
R2301:Gtf2a1l	UTSW	17	89,018,900 (GRCm39)	missense	probably benign
R2906:Gtf2a1l	UTSW	17	89,002,083 (GRCm39)	missense	possibly damaging	0.92
R4281:Gtf2a1l	UTSW	17	89,019,065 (GRCm39)	missense	possibly damaging	0.95
R4289:Gtf2a1l	UTSW	17	89,001,884 (GRCm39)	missense	probably damaging	0.98
R4771:Gtf2a1l	UTSW	17	88,997,448 (GRCm39)	missense	probably benign	0.23
R4904:Gtf2a1l	UTSW	17	88,997,471 (GRCm39)	critical splice donor site	probably null
R4941:Gtf2a1l	UTSW	17	89,022,350 (GRCm39)	missense	probably damaging	1.00
R5106:Gtf2a1l	UTSW	17	89,002,073 (GRCm39)	missense	possibly damaging	0.95
R6003:Gtf2a1l	UTSW	17	89,001,531 (GRCm39)	missense	probably damaging	1.00
R6035:Gtf2a1l	UTSW	17	89,018,962 (GRCm39)	missense	probably benign	0.00
R6035:Gtf2a1l	UTSW	17	89,018,962 (GRCm39)	missense	probably benign	0.00
R6128:Gtf2a1l	UTSW	17	89,002,086 (GRCm39)	missense	probably null	0.94
R6481:Gtf2a1l	UTSW	17	89,019,053 (GRCm39)	missense	probably benign	0.09
R7344:Gtf2a1l	UTSW	17	89,001,531 (GRCm39)	missense	probably damaging	1.00
R7462:Gtf2a1l	UTSW	17	89,001,566 (GRCm39)	missense	possibly damaging	0.77
R8712:Gtf2a1l	UTSW	17	89,022,351 (GRCm39)	missense	probably damaging	1.00
R8849:Gtf2a1l	UTSW	17	89,001,566 (GRCm39)	missense	possibly damaging	0.77
R9178:Gtf2a1l	UTSW	17	88,976,152 (GRCm39)	missense
R9407:Gtf2a1l	UTSW	17	89,001,531 (GRCm39)	missense	probably damaging	1.00
R9569:Gtf2a1l	UTSW	17	89,001,948 (GRCm39)	missense	probably benign
R9760:Gtf2a1l	UTSW	17	89,019,020 (GRCm39)	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- CACAGCCTGAGAAGTGACAC -3'
(R):5'- TCATAGAAAGGTGAGGCCCTC -3'

Sequencing Primer
(F):5'- CCTCCTTCAACTGTGTTAGGATATG -3'
(R):5'- TAGAAAGGTGAGGCCCTCTCTAC -3'

Posted On

2018-02-28