Mutagenetix > Incidental Mutation

Incidental Mutation 'R4675:Tfam'

349510

Institutional Source

Beutler Lab

Gene Symbol

Tfam

Ensembl Gene

ENSMUSG00000003923

Gene Name

transcription factor A, mitochondrial

Synonyms

Hmgts, tsHMG, mtTFA

MMRRC Submission

041930-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4675 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

71061294-71074110 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 71069225 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 166 (S166P)

Ref Sequence

ENSEMBL: ENSMUSP00000090086 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000092430] [ENSMUST00000105432] [ENSMUST00000121685] [ENSMUST00000152505]

AlphaFold

P40630

Predicted Effect

probably benign
Transcript: ENSMUST00000092430
AA Change: S166P

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000090086
Gene: ENSMUSG00000003923
AA Change: S166P

Domain	Start	End	E-Value	Type
HMG	48	118	4.91e-21	SMART
low complexity region	129	148	N/A	INTRINSIC
HMG	153	219	4.66e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000105432
AA Change: S138P

PolyPhen 2 Score 0.148 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000101072
Gene: ENSMUSG00000003923
AA Change: S138P

Domain	Start	End	E-Value	Type
HMG	20	90	4.91e-21	SMART
low complexity region	101	120	N/A	INTRINSIC
HMG	125	191	4.66e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000121685
AA Change: S122P

PolyPhen 2 Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000113581
Gene: ENSMUSG00000003923
AA Change: S122P

Domain	Start	End	E-Value	Type
HMG	4	74	4.91e-21	SMART
low complexity region	85	104	N/A	INTRINSIC
HMG	109	175	4.66e-13	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145220

Predicted Effect

probably benign
Transcript: ENSMUST00000152505
AA Change: S122P

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000120871
Gene: ENSMUSG00000003923
AA Change: S122P

Domain	Start	End	E-Value	Type
HMG	4	74	4.91e-21	SMART
low complexity region	85	104	N/A	INTRINSIC
Blast:HMG	109	143	6e-16	BLAST

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.9%

Validation Efficiency

95% (89/94)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a key mitochondrial transcription factor containing two high mobility group motifs. The encoded protein also functions in mitochondrial DNA replication and repair. Sequence polymorphisms in this gene are associated with Alzheimer's and Parkinson's diseases. There are pseudogenes for this gene on chromosomes 6, 7, and 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
PHENOTYPE: Homozygous null mutants exhibit retarded growth, abnormal somite development, lack of optic discs, cardiac defects and delayed neural development. Mutants die by embryonic day 10.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310061I04Rik	C	A	17: 36,203,820 (GRCm39)	K291N	probably damaging	Het
Adgra1	A	G	7: 139,456,102 (GRCm39)	T577A	probably damaging	Het
Akip1	T	A	7: 109,308,188 (GRCm39)	I152N	possibly damaging	Het
Armc9	A	G	1: 86,130,240 (GRCm39)	Y8C	probably damaging	Het
Atp1a4	A	T	1: 172,085,223 (GRCm39)	V66E	possibly damaging	Het
Atp2a3	A	T	11: 72,872,623 (GRCm39)	T724S	probably damaging	Het
Bmp1	C	A	14: 70,730,284 (GRCm39)	R416L	probably damaging	Het
Bmt2	G	T	6: 13,663,300 (GRCm39)	A66E	probably benign	Het
Bscl2	A	T	19: 8,825,523 (GRCm39)	D403V	possibly damaging	Het
Cbx2	T	A	11: 118,919,935 (GRCm39)	I500N	probably damaging	Het
Cd84	A	T	1: 171,700,887 (GRCm39)	H216L	possibly damaging	Het
Cdhr18	A	T	14: 13,856,724 (GRCm38)	D462E	probably benign	Het
Ceacam15	T	C	7: 16,407,410 (GRCm39)	T36A	probably benign	Het
Cebpd	A	G	16: 15,705,385 (GRCm39)	D66G	probably damaging	Het
Cntnap4	A	G	8: 113,512,468 (GRCm39)	Y610C	probably damaging	Het
Col11a2	T	C	17: 34,283,267 (GRCm39)		probably null	Het
Col17a1	T	C	19: 47,651,497 (GRCm39)		probably null	Het
Cracr2b	A	G	7: 141,043,451 (GRCm39)	D43G	probably damaging	Het
Dgkz	T	A	2: 91,768,691 (GRCm39)	K697*	probably null	Het
Dnah7b	T	A	1: 46,256,317 (GRCm39)	D1873E	possibly damaging	Het
Dst	G	A	1: 34,314,784 (GRCm39)	E6472K	possibly damaging	Het
Duox2	T	C	2: 122,111,414 (GRCm39)	D1428G	probably damaging	Het
Elmod2	T	C	8: 84,043,537 (GRCm39)	N210S	probably damaging	Het
Ephx1	A	G	1: 180,822,256 (GRCm39)	F220S	probably damaging	Het
F13b	A	G	1: 139,429,542 (GRCm39)	Y20C	unknown	Het
Fbn2	T	A	18: 58,173,265 (GRCm39)	N2051I	possibly damaging	Het
Gabrg2	G	A	11: 41,859,650 (GRCm39)	H201Y	probably damaging	Het
Gbgt1	T	C	2: 28,388,453 (GRCm39)	F46S	possibly damaging	Het
Gjd4	A	G	18: 9,280,578 (GRCm39)	S167P	probably damaging	Het
Heatr5a	T	C	12: 51,924,130 (GRCm39)	N2028D	probably benign	Het
Heca	T	C	10: 17,791,057 (GRCm39)	H333R	probably benign	Het
Herc1	T	C	9: 66,298,740 (GRCm39)	S625P	probably damaging	Het
Ighv1-55	T	C	12: 115,172,175 (GRCm39)		probably benign	Het
Ighv5-8	G	A	12: 113,618,777 (GRCm39)	S64N	probably benign	Het
Itga1	G	T	13: 115,138,227 (GRCm39)		probably null	Het
Kif21a	C	A	15: 90,824,748 (GRCm39)	R1342L	possibly damaging	Het
Ksr1	G	A	11: 78,965,186 (GRCm39)	P118S	possibly damaging	Het
Lat2	T	C	5: 134,634,911 (GRCm39)	N100S	probably damaging	Het
Lrit3	T	A	3: 129,582,121 (GRCm39)	D501V	probably damaging	Het
Lrrfip1	T	A	1: 91,031,042 (GRCm39)		probably null	Het
Lyst	G	A	13: 13,809,968 (GRCm39)	R546H	probably damaging	Het
Med21	T	A	6: 146,551,691 (GRCm39)	L114H	probably damaging	Het
Mfap4	A	T	11: 61,376,336 (GRCm39)		probably benign	Het
Mpdz	G	A	4: 81,302,049 (GRCm39)	R233W	probably damaging	Het
Mrc2	G	A	11: 105,239,257 (GRCm39)		probably null	Het
Ncapd3	T	C	9: 27,006,038 (GRCm39)		probably benign	Het
Neto2	T	G	8: 86,396,333 (GRCm39)	H104P	probably damaging	Het
Nr1h2	T	C	7: 44,201,979 (GRCm39)	T36A	possibly damaging	Het
Nudt16l2	T	C	9: 105,021,647 (GRCm39)	D133G	probably benign	Het
Or13a20	A	T	7: 140,232,074 (GRCm39)	M61L	probably damaging	Het
Or4a79	T	C	2: 89,551,838 (GRCm39)	I206V	probably benign	Het
Or51ab3	T	G	7: 103,201,183 (GRCm39)	L64V	probably damaging	Het
Or51g2	A	G	7: 102,623,013 (GRCm39)	M62T	probably damaging	Het
Or52p1	T	A	7: 104,267,631 (GRCm39)	C248*	probably null	Het
Or5p52	A	G	7: 107,502,567 (GRCm39)	I214M	probably damaging	Het
Or5p72	T	C	7: 108,022,309 (GRCm39)	V177A	possibly damaging	Het
Or8b4	T	C	9: 37,830,882 (GRCm39)	*310R	probably null	Het
Pcbp3	A	G	10: 76,606,869 (GRCm39)	L241S	possibly damaging	Het
Pcf11	G	A	7: 92,308,985 (GRCm39)		probably benign	Het
Podxl	G	A	6: 31,503,579 (GRCm39)	T254M	possibly damaging	Het
Prr27	A	C	5: 87,991,100 (GRCm39)	E237D	possibly damaging	Het
Rdh16	G	T	10: 127,637,316 (GRCm39)	V84F	probably damaging	Het
Rnf26	A	T	9: 44,023,428 (GRCm39)	D273E	probably benign	Het
Rpl13a	A	T	7: 44,776,242 (GRCm39)		probably benign	Het
Rpl3l	A	G	17: 24,952,584 (GRCm39)	K239E	probably benign	Het
Rsf1	A	AGGGCGACGG	7: 97,229,111 (GRCm39)		probably null	Het
Rsf1	G	A	7: 97,229,117 (GRCm39)		probably benign	Het
Ryk	A	G	9: 102,768,415 (GRCm39)	D352G	possibly damaging	Het
Setd1b	T	A	5: 123,299,061 (GRCm39)		probably benign	Het
Sh2b1	G	A	7: 126,070,618 (GRCm39)	A361V	possibly damaging	Het
Slc35f3	A	T	8: 127,047,935 (GRCm39)	K92*	probably null	Het
Slc39a10	A	G	1: 46,857,144 (GRCm39)		probably benign	Het
Slc47a1	G	A	11: 61,253,857 (GRCm39)	T194I	probably benign	Het
Slc6a3	C	A	13: 73,692,936 (GRCm39)	N185K	probably damaging	Het
Stag1	T	C	9: 100,730,758 (GRCm39)	V391A	probably damaging	Het
Syne2	A	C	12: 75,996,075 (GRCm39)	N2206T	probably damaging	Het
Tbc1d23	C	A	16: 57,003,325 (GRCm39)	R481I	possibly damaging	Het
Tcstv7b	T	C	13: 120,702,362 (GRCm39)	W53R	probably damaging	Het
Tmem63a	A	G	1: 180,784,056 (GRCm39)	H212R	probably benign	Het
Txndc11	T	A	16: 10,902,745 (GRCm39)	Q634L	possibly damaging	Het
Usp31	T	C	7: 121,306,548 (GRCm39)		probably benign	Het
Vmn1r204	A	T	13: 22,740,962 (GRCm39)	M198L	probably damaging	Het
Vmn2r17	A	T	5: 109,575,049 (GRCm39)	T119S	probably benign	Het
Vsig1	A	G	X: 139,833,861 (GRCm39)	D227G	probably damaging	Het
Zfhx2	G	A	14: 55,304,678 (GRCm39)	P1102L	probably benign	Het
Zfp715	T	C	7: 42,949,444 (GRCm39)	Q172R	probably benign	Het
Zfp872	A	G	9: 22,108,701 (GRCm39)	D53G	probably damaging	Het
Zswim8	G	A	14: 20,764,681 (GRCm39)	D684N	probably benign	Het

Other mutations in Tfam

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01773:Tfam	APN	10	71,072,805 (GRCm39)	missense	possibly damaging	0.56
PIT4142001:Tfam	UTSW	10	71,070,813 (GRCm39)	missense	possibly damaging	0.88
R1462:Tfam	UTSW	10	71,071,380 (GRCm39)	missense	probably damaging	1.00
R1462:Tfam	UTSW	10	71,071,380 (GRCm39)	missense	probably damaging	1.00
R4367:Tfam	UTSW	10	71,069,233 (GRCm39)	missense	probably damaging	1.00
R4684:Tfam	UTSW	10	71,073,677 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CTGCATGTGATAGCAACAGGAC -3'
(R):5'- TACAAATCCCACCGTGCTGG -3'

Sequencing Primer
(F):5'- ATGCACACTAAGCTGGTTCTG -3'
(R):5'- GCATCTGCACTGGGAAGTG -3'

Posted On

2015-10-08