Mutagenetix > Incidental Mutation

Incidental Mutation 'RF003:Vcpkmt'

602648

Institutional Source

Beutler Lab

Gene Symbol

Vcpkmt

Ensembl Gene

ENSMUSG00000049882

Gene Name

valosin containing protein lysine (K) methyltransferase

Synonyms

Gm71, Mettl21d, LOC207965

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

RF003 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

69624402-69629884 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 69629598 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 55 (T55S)

Ref Sequence

ENSEMBL: ENSMUSP00000055002 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000035773] [ENSMUST00000058639] [ENSMUST00000182396] [ENSMUST00000183277]

AlphaFold

Q8C436

Predicted Effect

probably benign
Transcript: ENSMUST00000035773

SMART Domains

Protein: ENSMUSP00000044866
Gene: ENSMUSG00000034801

Domain	Start	End	E-Value	Type
Pfam:Histone	54	169	3.7e-13	PFAM
RhoGEF	203	388	1.98e-35	SMART
PH	443	547	1.54e-14	SMART
RasGEFN	595	740	5.8e-52	SMART
RasGEF	775	1019	2.51e-92	SMART
low complexity region	1079	1099	N/A	INTRINSIC
low complexity region	1144	1152	N/A	INTRINSIC
low complexity region	1173	1192	N/A	INTRINSIC
low complexity region	1200	1225	N/A	INTRINSIC
low complexity region	1254	1269	N/A	INTRINSIC
low complexity region	1276	1292	N/A	INTRINSIC
low complexity region	1301	1309	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000058639
AA Change: T55S

PolyPhen 2 Score 0.481 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000055002
Gene: ENSMUSG00000049882
AA Change: T55S

Domain	Start	End	E-Value	Type
Pfam:Methyltransf_16	22	194	1.7e-57	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000182396

SMART Domains

Protein: ENSMUSP00000138589
Gene: ENSMUSG00000034801

Domain	Start	End	E-Value	Type
Pfam:Histone	97	169	1e-9	PFAM
Pfam:RhoGEF	203	344	1.6e-12	PFAM
PH	410	514	1.54e-14	SMART
RasGEFN	562	707	5.8e-52	SMART
RasGEF	742	986	2.51e-92	SMART
low complexity region	1046	1066	N/A	INTRINSIC
low complexity region	1111	1119	N/A	INTRINSIC
low complexity region	1140	1159	N/A	INTRINSIC
low complexity region	1167	1192	N/A	INTRINSIC
low complexity region	1221	1236	N/A	INTRINSIC
low complexity region	1243	1259	N/A	INTRINSIC
low complexity region	1268	1276	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000183277

SMART Domains

Protein: ENSMUSP00000138793
Gene: ENSMUSG00000034801

Domain	Start	End	E-Value	Type
Pfam:Histone	97	169	8.9e-11	PFAM
RhoGEF	203	388	1.98e-35	SMART
PH	443	547	1.54e-14	SMART
RasGEFN	595	740	5.8e-52	SMART
RasGEF	775	1019	2.51e-92	SMART
low complexity region	1079	1099	N/A	INTRINSIC
low complexity region	1144	1152	N/A	INTRINSIC
low complexity region	1173	1192	N/A	INTRINSIC
low complexity region	1200	1225	N/A	INTRINSIC
low complexity region	1254	1269	N/A	INTRINSIC
low complexity region	1276	1292	N/A	INTRINSIC
low complexity region	1301	1309	N/A	INTRINSIC

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.2%
20x: 98.1%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit no abnormal phenotype. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930433I11Rik	AACC	A	7: 40,642,479 (GRCm39)		probably benign	Het
A630073D07Rik	A	C	6: 132,604,406 (GRCm39)	L13R	unknown	Het
Alg9	GGC	GGCCGC	9: 50,686,727 (GRCm39)		probably benign	Het
Arb2a	A	T	13: 77,982,794 (GRCm39)	I135L	possibly damaging	Het
Arc	G	C	15: 74,543,980 (GRCm39)	T81S	probably benign	Het
Atad5	A	T	11: 80,002,386 (GRCm39)	K1059N	probably damaging	Het
Bdp1	C	A	13: 100,196,957 (GRCm39)	V1143F	probably benign	Het
Bdp1	C	A	13: 100,196,958 (GRCm39)	Q1142H	probably benign	Het
Ccdc33	T	C	9: 57,965,574 (GRCm39)	S583G	probably benign	Het
Cd109	TTAT	TTATTTATTTATATAT	9: 78,619,813 (GRCm39)		probably benign	Het
Cep192	A	T	18: 67,971,027 (GRCm39)	R1009S	probably benign	Het
Clvs2	T	A	10: 33,498,921 (GRCm39)	H3L	probably damaging	Het
Cnot6	T	C	11: 49,593,440 (GRCm39)	M14V	probably benign	Het
Colec10	A	G	15: 54,325,787 (GRCm39)	R206G	possibly damaging	Het
Dennd6a	T	C	14: 26,350,689 (GRCm39)	I598T	probably damaging	Het
Dmrt2	T	C	19: 25,655,498 (GRCm39)	S366P	probably damaging	Het
Dnmt1	AGTTCCTACCTCGTT	AGTTCCTACCTCGTTTTGGGGGCGGAGCACCGTTCCTACCTCGTT	9: 20,821,427 (GRCm39)		probably null	Het
Efhb	T	C	17: 53,707,919 (GRCm39)	D748G	probably damaging	Het
Etl4	C	T	2: 20,524,729 (GRCm39)	Q21*	probably null	Het
Flywch1	CCACTCCTGGTGT	CCACTCCTGGTGTGGGGAGGCTACGTACTCACACACTCCTGGTGT	17: 23,981,140 (GRCm39)		probably null	Het
Fmn1	ACCTCC	ACCTCCCCCTCC	2: 113,356,131 (GRCm39)		probably benign	Het
Fsip2	T	A	2: 82,821,865 (GRCm39)	M5866K	probably benign	Het
Gab3	CTT	CTTATT	X: 74,043,612 (GRCm39)		probably null	Het
Garin5a	C	CGGAGGGAGGAAGGCTGGATCCTGGATACCTGGGTA	7: 44,149,951 (GRCm39)		probably null	Het
Gnl2	T	A	4: 124,937,518 (GRCm39)		probably null	Het
Grip2	C	T	6: 91,760,574 (GRCm39)	R341Q	probably benign	Het
Hmcn1	T	A	1: 150,500,312 (GRCm39)	H3960L	probably damaging	Het
Igkv6-25	T	A	6: 70,192,762 (GRCm39)	Y56*	probably null	Het
Il12a	A	T	3: 68,602,562 (GRCm39)	T102S	probably benign	Het
Il1a	T	A	2: 129,144,852 (GRCm39)	I189F	possibly damaging	Het
Inpp4b	T	A	8: 82,696,150 (GRCm39)	Y361*	probably null	Het
Iqcf4	CTTTTCCTTTTCCTTTT	CTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCATTTTCCTTTTCCTTTT	9: 106,447,806 (GRCm39)		probably benign	Het
Irag2	AGCACATTG	AGCACATTGTGCACATTG	6: 145,119,509 (GRCm39)		probably benign	Het
Krt1	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	15: 101,758,813 (GRCm39)		probably benign	Het
Las1l	AGTGG	AGTGGTGG	X: 94,984,422 (GRCm39)		probably benign	Het
Lrrc8d	T	C	5: 105,960,507 (GRCm39)	Y306H	probably damaging	Het
Mamld1	AGC	AGCCGC	X: 70,162,426 (GRCm39)		probably benign	Het
Map1a	CTCCAGCTCCAGCTCCAGCTCCA	CTCCAGCTCCAGCTCCAGCTCCAGCTCCAGATCCAGCTCCAGCTCCAGCTCCA	2: 121,136,777 (GRCm39)		probably benign	Het
Map1b	G	T	13: 99,567,258 (GRCm39)	A1821E	unknown	Het
Maz	A	G	7: 126,624,669 (GRCm39)	C284R	probably damaging	Het
Med23	A	G	10: 24,779,683 (GRCm39)	H920R	probably damaging	Het
Megf10	CCAGCAGCAGCAGCAGCAGCAG	CCAGCAGCAGCAGCAGCAG	18: 57,427,099 (GRCm39)		probably benign	Het
Mmp14	C	T	14: 54,676,471 (GRCm39)	R339*	probably null	Het
Mroh9	T	G	1: 162,885,630 (GRCm39)	K334T	probably damaging	Het
Nab1	A	T	1: 52,518,441 (GRCm39)	C320S	probably damaging	Het
Noto	T	C	6: 85,401,192 (GRCm39)	S74P	probably benign	Het
Nudt4	T	C	10: 95,385,236 (GRCm39)	N152D	possibly damaging	Het
Nup155	T	TTTTG	15: 8,148,660 (GRCm39)		probably benign	Het
Nusap1	AGCTGAGA	AGCTGAGATACACGTTAGCAGTGAGGAGCAGGCTGAGA	2: 119,458,084 (GRCm39)		probably benign	Het
Or10al2	A	C	17: 37,983,749 (GRCm39)	K278N	probably damaging	Het
Or2d4	T	A	7: 106,543,855 (GRCm39)	M118L	probably damaging	Het
Or2t48	CA	C	11: 58,419,983 (GRCm39)		probably null	Het
Or51f1e	GTTAT	GTTATTAT	7: 102,747,512 (GRCm39)			Het
Or51f1e	TTA	TTAGTA	7: 102,747,513 (GRCm39)		probably null	Het
Or7g16	T	C	9: 18,726,778 (GRCm39)	T271A	probably benign	Het
Or9a7	T	C	6: 40,521,296 (GRCm39)	I206V	probably benign	Het
Plxnc1	T	C	10: 94,630,306 (GRCm39)	Y1531C	probably damaging	Het
Pnma8b	TGA	TGAAGA	7: 16,679,941 (GRCm39)		probably benign	Het
Rp1	A	G	1: 4,414,917 (GRCm39)	V2065A	probably damaging	Het
Sbp	AAGATGCTGACAACA	AAGATGCTGACAACAGAGATGCTGACAACA	17: 24,164,343 (GRCm39)		probably benign	Het
Sepsecs	G	A	5: 52,804,533 (GRCm39)	T379M	probably benign	Het
Sfswap	GGCC	GGCCCACTCTGCC	5: 129,646,828 (GRCm39)		probably benign	Het
Six3	GCG	GCGTCG	17: 85,928,798 (GRCm39)		probably benign	Het
Tfeb	C	T	17: 48,099,003 (GRCm39)	T259I	possibly damaging	Het
Tgoln1	A	AAACTCAG	6: 72,593,335 (GRCm39)		probably null	Het
Tmem94	G	A	11: 115,686,958 (GRCm39)	V1108M	probably damaging	Het
Usp35	T	C	7: 96,971,303 (GRCm39)	K297E	possibly damaging	Het
Zfp384	GCCCAGGCCCAG	GCCCAGGCCCAGTCCCAGGCCCAG	6: 125,013,446 (GRCm39)		probably benign	Het
Zfp384	GCCCAGGCCCAGGCCCAGGCCCAG	GCCCAGGCCCAGTCCCAGGCCCAGGCCCAGGCCCAG	6: 125,013,434 (GRCm39)		probably benign	Het
Zfp384	GGCCC	GGCCCTGGCCCAAGCCC	6: 125,013,439 (GRCm39)		probably benign	Het
Zfp407	A	T	18: 84,227,688 (GRCm39)	S1974T	probably benign	Het
Zfp677	T	C	17: 21,617,704 (GRCm39)	S254P	probably damaging	Het

Other mutations in Vcpkmt

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
PIT4131001:Vcpkmt	UTSW	12	69,629,552 (GRCm39)	missense	probably benign	0.01
R0519:Vcpkmt	UTSW	12	69,629,102 (GRCm39)	missense	probably benign	0.00
R1926:Vcpkmt	UTSW	12	69,629,519 (GRCm39)	missense	probably damaging	0.99
R6401:Vcpkmt	UTSW	12	69,629,619 (GRCm39)	missense	probably damaging	1.00
R9729:Vcpkmt	UTSW	12	69,627,936 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCAGTGACTATAACATCTGCCC -3'
(R):5'- ACTTTGAGAGTCACGCATGC -3'

Sequencing Primer
(F):5'- CCTCGTTGAGGTACAGGC -3'
(R):5'- AGTCACGCATGCGCCTTG -3'

Posted On

2019-12-04