Mutagenetix > Incidental Mutation

Incidental Mutation 'R1834:Tet1'

205070

Institutional Source

Beutler Lab

Gene Symbol

Tet1

Ensembl Gene

ENSMUSG00000047146

Gene Name

tet methylcytosine dioxygenase 1

Synonyms

Cxxc6, D10Ertd17e, 2510010B09Rik, BB001228

MMRRC Submission

039861-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1834 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

62640349-62723242 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 62649444 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 89 (P89S)

Ref Sequence

ENSEMBL: ENSMUSP00000134328 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000050826] [ENSMUST00000174121] [ENSMUST00000174189]

AlphaFold

Q3URK3

Predicted Effect

probably benign
Transcript: ENSMUST00000050826
AA Change: P1686S

PolyPhen 2 Score 0.188 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000059527
Gene: ENSMUSG00000047146
AA Change: P1686S

Domain	Start	End	E-Value	Type
low complexity region	8	21	N/A	INTRINSIC
low complexity region	118	132	N/A	INTRINSIC
low complexity region	553	564	N/A	INTRINSIC
Pfam:zf-CXXC	566	607	2.5e-11	PFAM
low complexity region	884	902	N/A	INTRINSIC
low complexity region	1087	1106	N/A	INTRINSIC
Tet_JBP	1528	1931	1e-171	SMART
low complexity region	1944	1956	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000173087
AA Change: P88S

SMART Domains

Protein: ENSMUSP00000133706
Gene: ENSMUSG00000047146
AA Change: P88S

Domain	Start	End	E-Value	Type
Tet_JBP	2	138	2.64e-3	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000173905

SMART Domains

Protein: ENSMUSP00000134571
Gene: ENSMUSG00000047146

Domain	Start	End	E-Value	Type
Pfam:Tet_JBP	1	61	2.4e-20	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000174121
AA Change: P89S

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000134328
Gene: ENSMUSG00000047146
AA Change: P89S

Domain	Start	End	E-Value	Type
Tet_JBP	1	352	1.49e-83	SMART
low complexity region	365	377	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000174189
AA Change: P1718S

PolyPhen 2 Score 0.206 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000133279
Gene: ENSMUSG00000047146
AA Change: P1718S

Domain	Start	End	E-Value	Type
low complexity region	8	21	N/A	INTRINSIC
low complexity region	118	132	N/A	INTRINSIC
low complexity region	553	564	N/A	INTRINSIC
Pfam:zf-CXXC	566	607	2.7e-10	PFAM
low complexity region	884	902	N/A	INTRINSIC
low complexity region	1087	1106	N/A	INTRINSIC
Tet_JBP	1528	1963	7.36e-170	SMART
low complexity region	1976	1988	N/A	INTRINSIC

Meta Mutation Damage Score

0.1536

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.1%
20x: 92.0%

Validation Efficiency

97% (116/119)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] DNA methylation is an epigenetic mechanism that is important for controlling gene expression. The protein encoded by this gene is a demethylase that belongs to the TET (ten-eleven translocation) family. Members of the TET protein family play a role in the DNA methylation process and gene activation. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit background sensitive lethality, abnormal forebrain development, abnormal female reproductive organs and decreased litter size. Mice homozygous for a different knock-out allele exhibit impaired adult neurogenesis, impaired spatial learning and impaired short-term memory retention. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 114 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310033P09Rik	A	G	11: 59,099,313 (GRCm39)	D20G	probably damaging	Het
2310061N02Rik	T	A	16: 88,504,786 (GRCm39)	S4C	unknown	Het
Abca3	A	T	17: 24,595,666 (GRCm39)	N340Y	probably benign	Het
Abcc1	A	G	16: 14,240,981 (GRCm39)	I513V	possibly damaging	Het
Acacb	C	T	5: 114,373,536 (GRCm39)	T1855M	probably damaging	Het
Ace	A	G	11: 105,876,920 (GRCm39)		probably benign	Het
Acss2	T	A	2: 155,400,550 (GRCm39)	Y530N	probably damaging	Het
Adarb1	C	A	10: 77,153,065 (GRCm39)		probably benign	Het
Afm	T	A	5: 90,674,283 (GRCm39)	M265K	probably benign	Het
Agl	A	G	3: 116,582,000 (GRCm39)	F293S	probably benign	Het
Aox1	G	A	1: 58,348,150 (GRCm39)	A623T	probably benign	Het
Arhgap31	C	A	16: 38,424,065 (GRCm39)	S667I	probably benign	Het
Bco1	A	G	8: 117,844,176 (GRCm39)	T297A	probably benign	Het
Bmp1	T	C	14: 70,746,271 (GRCm39)	S123G	possibly damaging	Het
Caps2	G	A	10: 112,031,623 (GRCm39)	D283N	possibly damaging	Het
Ccdc57	A	C	11: 120,752,045 (GRCm39)	S845R	probably benign	Het
Cd209f	A	G	8: 4,154,491 (GRCm39)	S119P	probably damaging	Het
Chrna6	A	G	8: 27,897,242 (GRCm39)	S212P	probably benign	Het
Col10a1	G	C	10: 34,271,011 (GRCm39)	A328P	probably damaging	Het
Col4a2	A	G	8: 11,452,997 (GRCm39)	E188G	probably benign	Het
Creb1	C	T	1: 64,590,109 (GRCm39)	Q32*	probably null	Het
Cttnbp2	C	T	6: 18,501,965 (GRCm39)	V16M	probably damaging	Het
D430041D05Rik	A	G	2: 103,998,446 (GRCm39)	S1102P	probably damaging	Het
Ddx31	C	T	2: 28,782,465 (GRCm39)	H603Y	probably damaging	Het
Ddx52	G	A	11: 83,850,323 (GRCm39)	C568Y	probably benign	Het
Dgki	C	A	6: 37,011,636 (GRCm39)		probably benign	Het
Dmrt1	A	T	19: 25,487,063 (GRCm39)	Q123L	probably damaging	Het
Dnah5	A	T	15: 28,409,270 (GRCm39)	M3563L	probably benign	Het
Dnah7b	A	T	1: 46,272,919 (GRCm39)	N2349I	possibly damaging	Het
Dscaml1	T	G	9: 45,594,930 (GRCm39)	S678A	probably benign	Het
Ece1	C	T	4: 137,685,312 (GRCm39)	R601W	probably damaging	Het
Ece1	A	G	4: 137,685,439 (GRCm39)	N643S	probably damaging	Het
Eno1b	A	G	18: 48,180,530 (GRCm39)	Y236C	probably damaging	Het
Esco1	T	C	18: 10,594,350 (GRCm39)	E312G	probably damaging	Het
Eya3	T	A	4: 132,434,429 (GRCm39)	V276E	probably damaging	Het
Fam161b	A	G	12: 84,395,552 (GRCm39)		probably benign	Het
Fem1c	C	T	18: 46,638,349 (GRCm39)	G551D	probably damaging	Het
Fer1l6	T	C	15: 58,429,718 (GRCm39)	I155T	possibly damaging	Het
Gbp7	A	G	3: 142,240,441 (GRCm39)	Y53C	probably damaging	Het
Gjb3	G	A	4: 127,220,224 (GRCm39)	R103W	probably damaging	Het
Gm10030	C	T	9: 110,833,947 (GRCm39)		noncoding transcript	Het
Gm3443	T	A	19: 21,533,043 (GRCm39)	H2Q	unknown	Het
Gm5800	T	C	14: 51,953,549 (GRCm39)	E22G	possibly damaging	Het
Gsdma2	G	T	11: 98,539,905 (GRCm39)	R9L	probably damaging	Het
Gvin3	A	T	7: 106,202,983 (GRCm39)	V87D	possibly damaging	Het
Ica1l	A	G	1: 60,067,395 (GRCm39)		probably benign	Het
Ice1	G	A	13: 70,763,457 (GRCm39)	T167I	probably damaging	Het
Ifi204	T	A	1: 173,575,172 (GRCm39)	R618S	unknown	Het
Itga2	C	A	13: 114,993,262 (GRCm39)	K784N	probably damaging	Het
Itga2	T	A	13: 114,993,263 (GRCm39)	K784M	probably damaging	Het
Kif3b	A	G	2: 153,159,405 (GRCm39)	E402G	probably benign	Het
Lrp2	T	C	2: 69,297,224 (GRCm39)	I3246V	probably benign	Het
Lrrn3	G	T	12: 41,503,517 (GRCm39)	L267I	probably damaging	Het
Map1s	A	G	8: 71,369,055 (GRCm39)	Y868C	probably damaging	Het
Mcm5	A	G	8: 75,845,901 (GRCm39)	T370A	possibly damaging	Het
Nat8f7	T	C	6: 85,684,793 (GRCm39)	S16G	probably benign	Het
Nav3	T	C	10: 109,555,883 (GRCm39)	T1683A	probably damaging	Het
Nbeal2	T	C	9: 110,456,197 (GRCm39)	N2417S	probably damaging	Het
Neb	T	C	2: 52,126,907 (GRCm39)	N3605S	probably damaging	Het
Net1	A	T	13: 3,962,941 (GRCm39)		probably benign	Het
Nsd1	A	G	13: 55,461,164 (GRCm39)	T2464A	possibly damaging	Het
Nt5e	T	A	9: 88,252,240 (GRCm39)	I534N	probably damaging	Het
Nudt12	T	A	17: 59,318,071 (GRCm39)	H58L	probably damaging	Het
Ocrl	T	A	X: 47,050,993 (GRCm39)	I74N	probably damaging	Het
Or1a1	A	G	11: 74,086,479 (GRCm39)	H50R	probably benign	Het
Or2ag13	A	G	7: 106,473,348 (GRCm39)	Y35H	probably damaging	Het
Or5ae2	A	G	7: 84,505,690 (GRCm39)	T38A	probably damaging	Het
Or9k2b	A	G	10: 130,016,701 (GRCm39)	I16T	probably benign	Het
Pef1	C	A	4: 130,014,966 (GRCm39)	C10*	probably null	Het
Phf21b	A	G	15: 84,681,547 (GRCm39)	Y256H	probably damaging	Het
Phox2a	G	T	7: 101,470,152 (GRCm39)		probably null	Het
Pi16	A	G	17: 29,546,419 (GRCm39)	E399G	possibly damaging	Het
Pipox	A	T	11: 77,772,949 (GRCm39)	Y321N	probably damaging	Het
Plin4	A	G	17: 56,410,522 (GRCm39)	S1170P	probably damaging	Het
Pnma2	C	T	14: 67,154,662 (GRCm39)	S362L	possibly damaging	Het
Ppp1r9a	T	C	6: 5,113,710 (GRCm39)	I738T	probably damaging	Het
Prkcsh	A	T	9: 21,919,634 (GRCm39)	K188M	probably damaging	Het
Rcc1l	A	T	5: 134,192,498 (GRCm39)	Y309N	probably damaging	Het
Ripk1	A	G	13: 34,199,196 (GRCm39)	T123A	probably benign	Het
Robo4	A	G	9: 37,324,355 (GRCm39)	D961G	probably benign	Het
Rps27a	A	G	11: 29,496,299 (GRCm39)	Y105H	probably benign	Het
Scaper	A	G	9: 55,724,018 (GRCm39)	Y641H	possibly damaging	Het
Scn1a	C	A	2: 66,154,960 (GRCm39)	Q666H	probably benign	Het
Scn1a	T	A	2: 66,154,961 (GRCm39)	Q666L	probably benign	Het
Sdhaf4	T	C	1: 24,042,234 (GRCm39)		probably null	Het
Sec14l3	A	G	11: 4,016,510 (GRCm39)		probably benign	Het
Selp	C	A	1: 163,955,729 (GRCm39)		probably null	Het
Sim1	A	G	10: 50,785,924 (GRCm39)	D259G	probably damaging	Het
Sptan1	T	A	2: 29,882,013 (GRCm39)		probably benign	Het
Sptbn4	T	A	7: 27,066,071 (GRCm39)	E679V	probably null	Het
Sytl3	G	A	17: 6,995,726 (GRCm39)	E169K	probably benign	Het
Taar1	T	C	10: 23,797,087 (GRCm39)	C262R	probably benign	Het
Taf7l2	T	C	10: 115,948,570 (GRCm39)	R319G	probably benign	Het
Tbc1d32	A	G	10: 55,893,700 (GRCm39)	I1291T	probably benign	Het
Tgfbrap1	C	A	1: 43,110,795 (GRCm39)	G7W	probably damaging	Het
Thada	A	G	17: 84,533,432 (GRCm39)	V1673A	possibly damaging	Het
Thbs4	A	G	13: 92,897,989 (GRCm39)	V610A	probably benign	Het
Tmem163	A	G	1: 127,605,246 (GRCm39)	S41P	probably benign	Het
Tmem65	A	T	15: 58,658,962 (GRCm39)	H200Q	probably damaging	Het
Trgc3	A	G	13: 19,447,535 (GRCm39)	T163A	possibly damaging	Het
Trim62	T	C	4: 128,803,018 (GRCm39)	V356A	possibly damaging	Het
Ttn	T	C	2: 76,562,502 (GRCm39)	D28781G	probably damaging	Het
Ttn	C	T	2: 76,593,604 (GRCm39)	V20679I	probably benign	Het
Tut7	A	T	13: 59,962,749 (GRCm39)	Y339*	probably null	Het
Unc80	A	T	1: 66,678,407 (GRCm39)	T2063S	possibly damaging	Het
Vav3	A	G	3: 109,413,742 (GRCm39)	T227A	probably benign	Het
Vmn2r118	A	T	17: 55,899,456 (GRCm39)	I816N	probably damaging	Het
Vmn2r26	T	A	6: 124,038,369 (GRCm39)	M648K	possibly damaging	Het
Vmn2r88	T	G	14: 51,650,487 (GRCm39)		probably benign	Het
Vwa3a	A	G	7: 120,389,359 (GRCm39)	T66A	probably benign	Het
Xirp2	T	A	2: 67,341,484 (GRCm39)	Y1242N	probably damaging	Het
Ywhag	G	A	5: 135,940,384 (GRCm39)	T70M	probably damaging	Het
Zfp248	T	C	6: 118,405,931 (GRCm39)	T452A	probably damaging	Het
Zfp988	A	T	4: 147,417,344 (GRCm39)	I593F	probably damaging	Het

Other mutations in Tet1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00539:Tet1	APN	10	62,650,276 (GRCm39)	missense	probably damaging	1.00
IGL01079:Tet1	APN	10	62,715,252 (GRCm39)	missense	probably damaging	0.99
IGL01109:Tet1	APN	10	62,715,553 (GRCm39)	missense	probably benign
IGL01634:Tet1	APN	10	62,714,367 (GRCm39)	missense	possibly damaging	0.94
IGL02003:Tet1	APN	10	62,652,179 (GRCm39)	missense	possibly damaging	0.92
IGL02081:Tet1	APN	10	62,649,597 (GRCm39)	missense	probably damaging	1.00
IGL02100:Tet1	APN	10	62,648,507 (GRCm39)	missense	possibly damaging	0.92
IGL02228:Tet1	APN	10	62,649,513 (GRCm39)	missense	probably damaging	0.99
IGL02524:Tet1	APN	10	62,714,425 (GRCm39)	missense	probably damaging	1.00
IGL02539:Tet1	APN	10	62,648,798 (GRCm39)	missense	possibly damaging	0.60
IGL02608:Tet1	APN	10	62,674,866 (GRCm39)	missense	probably damaging	1.00
IGL02608:Tet1	APN	10	62,715,388 (GRCm39)	missense	possibly damaging	0.82
IGL02702:Tet1	APN	10	62,715,531 (GRCm39)	missense	possibly damaging	0.83
K7371:Tet1	UTSW	10	62,714,955 (GRCm39)	missense	probably benign
R0166:Tet1	UTSW	10	62,676,058 (GRCm39)	missense	probably benign	0.05
R0371:Tet1	UTSW	10	62,714,178 (GRCm39)	missense	probably damaging	0.97
R0373:Tet1	UTSW	10	62,713,988 (GRCm39)	nonsense	probably null
R0391:Tet1	UTSW	10	62,650,325 (GRCm39)	splice site	probably null
R0445:Tet1	UTSW	10	62,715,720 (GRCm39)	missense	probably benign	0.08
R1016:Tet1	UTSW	10	62,715,729 (GRCm39)	missense	probably benign
R1344:Tet1	UTSW	10	62,650,300 (GRCm39)	missense	probably damaging	1.00
R1546:Tet1	UTSW	10	62,648,689 (GRCm39)	missense	probably damaging	1.00
R1651:Tet1	UTSW	10	62,715,453 (GRCm39)	missense	probably damaging	1.00
R1725:Tet1	UTSW	10	62,650,256 (GRCm39)	missense	probably damaging	1.00
R1752:Tet1	UTSW	10	62,648,768 (GRCm39)	missense	probably damaging	0.99
R1964:Tet1	UTSW	10	62,648,726 (GRCm39)	missense	possibly damaging	0.86
R2239:Tet1	UTSW	10	62,715,513 (GRCm39)	missense	probably benign	0.01
R2962:Tet1	UTSW	10	62,650,323 (GRCm39)	nonsense	probably null
R3084:Tet1	UTSW	10	62,715,400 (GRCm39)	missense	probably benign	0.34
R3086:Tet1	UTSW	10	62,715,400 (GRCm39)	missense	probably benign	0.34
R3972:Tet1	UTSW	10	62,649,505 (GRCm39)	missense	probably damaging	1.00
R4622:Tet1	UTSW	10	62,655,253 (GRCm39)	missense	possibly damaging	0.92
R4674:Tet1	UTSW	10	62,674,627 (GRCm39)	missense	probably damaging	0.97
R4687:Tet1	UTSW	10	62,674,570 (GRCm39)	missense	probably benign	0.04
R4718:Tet1	UTSW	10	62,649,591 (GRCm39)	missense	probably damaging	0.96
R4801:Tet1	UTSW	10	62,658,442 (GRCm39)	missense	probably damaging	0.99
R4802:Tet1	UTSW	10	62,658,442 (GRCm39)	missense	probably damaging	0.99
R4903:Tet1	UTSW	10	62,658,437 (GRCm39)	missense	probably damaging	1.00
R5153:Tet1	UTSW	10	62,714,357 (GRCm39)	missense	possibly damaging	0.85
R5193:Tet1	UTSW	10	62,674,026 (GRCm39)	missense	probably benign	0.22
R5225:Tet1	UTSW	10	62,674,450 (GRCm39)	missense	probably damaging	1.00
R5437:Tet1	UTSW	10	62,650,230 (GRCm39)	missense	probably benign	0.01
R5465:Tet1	UTSW	10	62,675,556 (GRCm39)	missense	probably benign
R5535:Tet1	UTSW	10	62,668,686 (GRCm39)	missense	probably damaging	1.00
R5586:Tet1	UTSW	10	62,714,073 (GRCm39)	missense	probably damaging	1.00
R5763:Tet1	UTSW	10	62,675,847 (GRCm39)	missense	probably damaging	1.00
R5788:Tet1	UTSW	10	62,675,737 (GRCm39)	missense	possibly damaging	0.70
R5818:Tet1	UTSW	10	62,652,187 (GRCm39)	missense	possibly damaging	0.71
R5860:Tet1	UTSW	10	62,648,399 (GRCm39)	splice site	probably null
R5975:Tet1	UTSW	10	62,715,552 (GRCm39)	missense	probably benign	0.37
R6041:Tet1	UTSW	10	62,649,152 (GRCm39)	missense	probably damaging	0.98
R6092:Tet1	UTSW	10	62,649,494 (GRCm39)	missense	probably benign	0.10
R6132:Tet1	UTSW	10	62,649,079 (GRCm39)	missense	probably damaging	0.99
R6157:Tet1	UTSW	10	62,675,749 (GRCm39)	missense	probably damaging	0.98
R6520:Tet1	UTSW	10	62,715,792 (GRCm39)	start codon destroyed	probably null	0.53
R7210:Tet1	UTSW	10	62,650,280 (GRCm39)	missense	probably null	0.95
R7223:Tet1	UTSW	10	62,649,450 (GRCm39)	missense	possibly damaging	0.95
R7255:Tet1	UTSW	10	62,658,415 (GRCm39)	missense	probably benign	0.15
R7323:Tet1	UTSW	10	62,715,818 (GRCm39)	start gained	probably benign
R7472:Tet1	UTSW	10	62,649,129 (GRCm39)	missense	possibly damaging	0.84
R7507:Tet1	UTSW	10	62,668,671 (GRCm39)	critical splice donor site	probably null
R7522:Tet1	UTSW	10	62,654,762 (GRCm39)	missense	possibly damaging	0.82
R7849:Tet1	UTSW	10	62,655,252 (GRCm39)	missense	possibly damaging	0.83
R7879:Tet1	UTSW	10	62,714,825 (GRCm39)	missense	probably benign	0.03
R8073:Tet1	UTSW	10	62,649,132 (GRCm39)	missense	probably damaging	0.98
R8098:Tet1	UTSW	10	62,714,859 (GRCm39)	missense	probably damaging	1.00
R8147:Tet1	UTSW	10	62,714,586 (GRCm39)	missense	probably benign	0.01
R8355:Tet1	UTSW	10	62,652,229 (GRCm39)	missense	possibly damaging	0.89
R8545:Tet1	UTSW	10	62,648,718 (GRCm39)	missense	probably damaging	1.00
R8556:Tet1	UTSW	10	62,675,985 (GRCm39)	missense	probably benign	0.37
R8936:Tet1	UTSW	10	62,676,063 (GRCm39)	nonsense	probably null
R9173:Tet1	UTSW	10	62,676,065 (GRCm39)	missense	probably benign
R9414:Tet1	UTSW	10	62,674,935 (GRCm39)	missense	probably benign	0.01
R9584:Tet1	UTSW	10	62,655,306 (GRCm39)	missense	probably damaging	1.00
Z1177:Tet1	UTSW	10	62,654,764 (GRCm39)	missense	possibly damaging	0.91

Predicted Primers

PCR Primer
(F):5'- AAGCTCTTAGTGTTGTGTGAACC -3'
(R):5'- TCCCTCAGGTGTGTACGTTG -3'

Sequencing Primer
(F):5'- TCTCACTGGTAGTTCATAGACAC -3'
(R):5'- TGATTCGAGCAGATGGCC -3'

Posted On

2014-06-23