Mutagenetix > Incidental Mutation

Incidental Mutation 'R6944:Tom1l2'

540789

Institutional Source

Beutler Lab

Gene Symbol

Tom1l2

Ensembl Gene

ENSMUSG00000000538

Gene Name

target of myb1-like 2 (chicken)

Synonyms

2900016I08Rik, A730055F12Rik, myb1-like protein 2

MMRRC Submission

045058-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.244) question?

Stock #

R6944 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

60117540-60243731 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 60139817 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 239 (V239A)

Ref Sequence

ENSEMBL: ENSMUSP00000090736 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000064019] [ENSMUST00000093046] [ENSMUST00000093048] [ENSMUST00000095254] [ENSMUST00000102682] [ENSMUST00000102683]

AlphaFold

Q5SRX1

Predicted Effect

probably damaging
Transcript: ENSMUST00000064019
AA Change: V284A

PolyPhen 2 Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000063414
Gene: ENSMUSG00000000538
AA Change: V284A

Domain	Start	End	E-Value	Type
VHS	13	148	1.88e-68	SMART
low complexity region	187	202	N/A	INTRINSIC
Pfam:GAT	216	317	1.7e-36	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000093046
AA Change: V234A

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000090734
Gene: ENSMUSG00000000538
AA Change: V234A

Domain	Start	End	E-Value	Type
Pfam:VHS	7	73	1.3e-19	PFAM
low complexity region	137	152	N/A	INTRINSIC
Pfam:GAT	166	267	3e-36	PFAM
low complexity region	428	443	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000093048
AA Change: V239A

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000090736
Gene: ENSMUSG00000000538
AA Change: V239A

Domain	Start	End	E-Value	Type
VHS	13	154	1.8e-47	SMART
Pfam:GAT	171	272	3e-36	PFAM
low complexity region	433	448	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000095254
AA Change: V284A

PolyPhen 2 Score 0.843 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000092884
Gene: ENSMUSG00000000538
AA Change: V284A

Domain	Start	End	E-Value	Type
VHS	13	148	1.88e-68	SMART
low complexity region	187	202	N/A	INTRINSIC
Pfam:GAT	216	317	2e-36	PFAM
low complexity region	458	473	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102682
AA Change: V284A

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000099743
Gene: ENSMUSG00000000538
AA Change: V284A

Domain	Start	End	E-Value	Type
VHS	13	148	1.88e-68	SMART
low complexity region	187	202	N/A	INTRINSIC
Pfam:GAT	216	317	1.7e-36	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102683
AA Change: V284A

PolyPhen 2 Score 0.634 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000099744
Gene: ENSMUSG00000000538
AA Change: V284A

Domain	Start	End	E-Value	Type
VHS	13	148	1.88e-68	SMART
low complexity region	187	202	N/A	INTRINSIC
Pfam:GAT	232	308	1e-26	PFAM
low complexity region	478	493	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000133420

SMART Domains

Protein: ENSMUSP00000117623
Gene: ENSMUSG00000000538

Domain	Start	End	E-Value	Type
low complexity region	170	185	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000143124

SMART Domains

Protein: ENSMUSP00000121936
Gene: ENSMUSG00000000538

Domain	Start	End	E-Value	Type
low complexity region	150	165	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.2%

Validation Efficiency

97% (75/77)

MGI Phenotype

PHENOTYPE: Mice homozygous for a hypomorphic gene trap allele show malocclusion, kyphosis, hydrocephaly, patchy hair, splenomegaly, high B- and T-cell counts, thrombopenia, impaired humoral responses, a high frequency of infections and tumors, renal cysts, skin lesions, freezing behavior and sporadic bleeding. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1b	T	G	5: 8,863,693 (GRCm39)	V216G	probably damaging	Het
Abcb5	T	C	12: 118,875,265 (GRCm39)	R636G	probably benign	Het
Ago1	G	T	4: 126,354,215 (GRCm39)	F198L	possibly damaging	Het
Ankrd42	C	T	7: 92,268,755 (GRCm39)		probably null	Het
Anxa11	T	A	14: 25,875,176 (GRCm39)	F274I	probably damaging	Het
Ascc1	T	C	10: 59,849,475 (GRCm39)	L122P	probably damaging	Het
Bptf	T	C	11: 106,971,649 (GRCm39)	S953G	probably damaging	Het
Chml	T	A	1: 175,515,727 (GRCm39)	N65Y	probably damaging	Het
Clcc1	A	G	3: 108,578,284 (GRCm39)	K262E	probably damaging	Het
Clhc1	T	G	11: 29,519,346 (GRCm39)	D384E	probably damaging	Het
Cnot2	G	A	10: 116,373,128 (GRCm39)		probably benign	Het
Cntnap1	T	C	11: 101,073,730 (GRCm39)	V627A	probably damaging	Het
Col6a4	A	G	9: 105,949,370 (GRCm39)	V755A	probably damaging	Het
Cyp4f18	T	A	8: 72,743,738 (GRCm39)	I406F	probably benign	Het
Dclre1a	T	C	19: 56,533,451 (GRCm39)	E381G	possibly damaging	Het
Dnah1	A	G	14: 30,990,861 (GRCm39)	Y3153H	probably damaging	Het
Dnah8	C	A	17: 31,013,633 (GRCm39)	D3791E	probably benign	Het
Dnah9	T	C	11: 65,975,975 (GRCm39)	E1358G	possibly damaging	Het
Eef1g	G	A	19: 8,945,656 (GRCm39)	R30H	probably benign	Het
Egln3	A	T	12: 54,230,738 (GRCm39)	I181N	probably benign	Het
Entpd6	A	G	2: 150,605,519 (GRCm39)	T250A	probably damaging	Het
Epb41l5	C	T	1: 119,536,859 (GRCm39)	R344Q	probably damaging	Het
Fam20b	T	C	1: 156,515,091 (GRCm39)	D258G	probably benign	Het
Fbxw18	A	T	9: 109,531,655 (GRCm39)	D21E	probably damaging	Het
Fbxw21	T	C	9: 108,986,603 (GRCm39)	E92G	probably damaging	Het
Fzd6	T	A	15: 38,889,212 (GRCm39)	M110K	possibly damaging	Het
Golgb1	C	T	16: 36,732,475 (GRCm39)	P574L	probably benign	Het
Gpr153	A	G	4: 152,363,820 (GRCm39)	E80G	probably damaging	Het
Gvin2	G	A	7: 105,551,187 (GRCm39)	Q622*	probably null	Het
Kcnt1	T	C	2: 25,767,840 (GRCm39)		probably benign	Het
Kcnt2	T	G	1: 140,511,803 (GRCm39)	V962G	probably benign	Het
Malt1	T	C	18: 65,570,991 (GRCm39)	V109A	probably benign	Het
Marchf7	A	G	2: 60,064,587 (GRCm39)	I288V	probably benign	Het
Mief1	C	T	15: 80,133,644 (GRCm39)	R234C	probably damaging	Het
Morc3	A	G	16: 93,667,460 (GRCm39)	S613G	probably benign	Het
Myt1	A	G	2: 181,439,387 (GRCm39)	E345G	possibly damaging	Het
Napb	T	C	2: 148,548,889 (GRCm39)	T133A	probably benign	Het
Nwd1	T	C	8: 73,380,162 (GRCm39)	V16A	possibly damaging	Het
Oas1f	G	A	5: 120,986,247 (GRCm39)	E67K	probably benign	Het
Obscn	T	C	11: 58,929,756 (GRCm39)	K5153R	probably damaging	Het
Or2w3b	T	A	11: 58,623,068 (GRCm39)	S308C	possibly damaging	Het
Or5a3	G	T	19: 12,400,628 (GRCm39)	M318I	probably benign	Het
Or5g26	C	T	2: 85,494,195 (GRCm39)	M194I	probably benign	Het
Or6d12	T	C	6: 116,492,791 (GRCm39)	F18L	possibly damaging	Het
Pdcd2	T	C	17: 15,745,632 (GRCm39)	N185S	possibly damaging	Het
Pgap1	A	T	1: 54,569,320 (GRCm39)	W349R	probably damaging	Het
Prpf39	T	A	12: 65,089,454 (GRCm39)	V64E	probably benign	Het
Ptpn13	T	A	5: 103,624,857 (GRCm39)	W54R	probably null	Het
Rbms3	G	T	9: 116,939,173 (GRCm39)	P29Q	probably damaging	Het
Rnf123	A	G	9: 107,940,822 (GRCm39)	L679P	probably benign	Het
Samd4	T	A	14: 47,254,092 (GRCm39)	D84E	possibly damaging	Het
Scarf1	T	C	11: 75,413,032 (GRCm39)	V426A	probably benign	Het
Slc12a1	A	G	2: 125,002,454 (GRCm39)	N145D	probably damaging	Het
Slc2a6	A	T	2: 26,916,076 (GRCm39)	M99K	probably damaging	Het
Slc34a2	A	T	5: 53,222,225 (GRCm39)	I306L	probably benign	Het
Slx4ip	A	G	2: 136,910,195 (GRCm39)	K397E	probably damaging	Het
Smr3a	C	T	5: 88,155,949 (GRCm39)		probably benign	Het
Spata31h1	A	C	10: 82,132,056 (GRCm39)	I318R	probably benign	Het
Spef2	T	C	15: 9,592,835 (GRCm39)	E1502G	probably damaging	Het
Sri	A	T	5: 8,113,365 (GRCm39)	T119S	probably benign	Het
Synrg	T	A	11: 83,915,912 (GRCm39)	L1085H	probably damaging	Het
Taf7	A	T	18: 37,775,910 (GRCm39)	L219H	probably damaging	Het
Tmco3	T	A	8: 13,353,729 (GRCm39)	V347E	probably damaging	Het
Tmem8b	A	T	4: 43,674,465 (GRCm39)	I250F	probably damaging	Het
Trpm1	T	A	7: 63,893,181 (GRCm39)	M1011K	probably damaging	Het
Tspan9	A	T	6: 127,942,769 (GRCm39)	Y153N	probably benign	Het
Ttll11	T	C	2: 35,642,306 (GRCm39)	H675R	probably benign	Het
Unc50	C	T	1: 37,471,743 (GRCm39)	T131M	probably damaging	Het
Vgf	T	A	5: 137,061,206 (GRCm39)	I456N	probably damaging	Het
Vmn1r223	A	G	13: 23,433,483 (GRCm39)	I26V	unknown	Het
Vmn1r39	T	C	6: 66,782,205 (GRCm39)	M1V	probably null	Het
Vmn2r111	T	C	17: 22,778,032 (GRCm39)	N549S	possibly damaging	Het
Vmn2r14	T	C	5: 109,363,925 (GRCm39)	T664A	probably benign	Het
Vmn2r14	G	A	5: 109,364,140 (GRCm39)	T592I	probably benign	Het
Vmn2r96	T	A	17: 18,817,891 (GRCm39)	F489L	probably benign	Het
Vmn2r-ps158	T	C	7: 42,697,393 (GRCm39)	F817L	possibly damaging	Het

Other mutations in Tom1l2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00648:Tom1l2	APN	11	60,151,942 (GRCm39)	missense	possibly damaging	0.93
IGL01459:Tom1l2	APN	11	60,171,095 (GRCm39)	missense	probably damaging	1.00
IGL02990:Tom1l2	APN	11	60,121,062 (GRCm39)	missense	probably damaging	1.00
R0025:Tom1l2	UTSW	11	60,120,960 (GRCm39)	missense	probably damaging	0.96
R0025:Tom1l2	UTSW	11	60,120,960 (GRCm39)	missense	probably damaging	0.96
R4456:Tom1l2	UTSW	11	60,243,641 (GRCm39)	unclassified	probably benign
R4627:Tom1l2	UTSW	11	60,133,533 (GRCm39)	critical splice donor site	probably null
R4695:Tom1l2	UTSW	11	60,161,259 (GRCm39)	missense	probably damaging	0.98
R4713:Tom1l2	UTSW	11	60,161,259 (GRCm39)	missense	probably damaging	0.98
R4731:Tom1l2	UTSW	11	60,161,259 (GRCm39)	missense	probably damaging	0.98
R4788:Tom1l2	UTSW	11	60,139,844 (GRCm39)	missense	probably damaging	1.00
R4937:Tom1l2	UTSW	11	60,149,744 (GRCm39)	missense	probably damaging	1.00
R5320:Tom1l2	UTSW	11	60,133,648 (GRCm39)	nonsense	probably null
R5367:Tom1l2	UTSW	11	60,132,634 (GRCm39)	missense	probably benign	0.00
R6158:Tom1l2	UTSW	11	60,123,753 (GRCm39)	missense	probably damaging	1.00
R7335:Tom1l2	UTSW	11	60,135,991 (GRCm39)	missense	probably benign	0.00
R7356:Tom1l2	UTSW	11	60,139,853 (GRCm39)	missense	probably damaging	0.99
R7376:Tom1l2	UTSW	11	60,152,026 (GRCm39)	missense	probably benign
R7544:Tom1l2	UTSW	11	60,171,040 (GRCm39)	small deletion	probably benign
R7760:Tom1l2	UTSW	11	60,165,791 (GRCm39)	missense	probably benign
R9200:Tom1l2	UTSW	11	60,120,942 (GRCm39)	missense	probably benign	0.37
R9291:Tom1l2	UTSW	11	60,153,556 (GRCm39)	missense	probably benign	0.09
R9394:Tom1l2	UTSW	11	60,132,715 (GRCm39)	missense	probably benign	0.00
R9514:Tom1l2	UTSW	11	60,153,486 (GRCm39)	missense	probably damaging	0.96
R9622:Tom1l2	UTSW	11	60,151,942 (GRCm39)	missense	possibly damaging	0.93
R9625:Tom1l2	UTSW	11	60,161,277 (GRCm39)	missense	probably damaging	1.00
Z1186:Tom1l2	UTSW	11	60,132,682 (GRCm39)	missense	probably benign	0.01
Z1187:Tom1l2	UTSW	11	60,132,682 (GRCm39)	missense	probably benign	0.01
Z1188:Tom1l2	UTSW	11	60,132,682 (GRCm39)	missense	probably benign	0.01
Z1189:Tom1l2	UTSW	11	60,132,682 (GRCm39)	missense	probably benign	0.01
Z1190:Tom1l2	UTSW	11	60,132,682 (GRCm39)	missense	probably benign	0.01
Z1191:Tom1l2	UTSW	11	60,132,682 (GRCm39)	missense	probably benign	0.01
Z1192:Tom1l2	UTSW	11	60,132,682 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- TCCAAGAGCAAATGAGCATCTC -3'
(R):5'- ACAAGCATGTACTCCTTCTGTG -3'

Sequencing Primer
(F):5'- GCAAATGAGCATCTCTGATGAC -3'
(R):5'- CTGTGACTTTCAAGAAACAGTGC -3'

Posted On

2018-11-28