Mutagenetix > Incidental Mutation

Incidental Mutation 'R5454:Pcmt1'

432679

Institutional Source

Beutler Lab

Gene Symbol

Pcmt1

Ensembl Gene

ENSMUSG00000019795

Gene Name

protein-L-isoaspartate (D-aspartate) O-methyltransferase 1

Synonyms

protein carboxyl methyltransferase, PIMT

MMRRC Submission

043018-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.170) question?

Stock #

R5454 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

7505137-7556900 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 7516509 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 167 (V167A)

Ref Sequence

ENSEMBL: ENSMUSP00000125144 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000159917] [ENSMUST00000161123] [ENSMUST00000162606] [ENSMUST00000162682] [ENSMUST00000163085]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000159917
AA Change: V181A

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000124932
Gene: ENSMUSG00000019795
AA Change: V181A

Domain	Start	End	E-Value	Type
low complexity region	7	25	N/A	INTRINSIC
Pfam:PCMT	66	279	1.1e-88	PFAM
Pfam:Ubie_methyltran	126	258	3.4e-7	PFAM
Pfam:Methyltransf_31	134	284	1.1e-8	PFAM
Pfam:Methyltransf_18	136	241	3e-9	PFAM
Pfam:Methyltransf_11	141	239	1.5e-6	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160250

Predicted Effect

probably benign
Transcript: ENSMUST00000161123

SMART Domains

Protein: ENSMUSP00000124100
Gene: ENSMUSG00000019795

Domain	Start	End	E-Value	Type
transmembrane domain	15	37	N/A	INTRINSIC
Pfam:PCMT	53	108	4.2e-14	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000161428
AA Change: V104A

SMART Domains

Protein: ENSMUSP00000123758
Gene: ENSMUSG00000019795
AA Change: V104A

Domain	Start	End	E-Value	Type
Pfam:PCMT	1	160	2.7e-61	PFAM
Pfam:Ubie_methyltran	49	148	8.3e-7	PFAM
Pfam:Methyltransf_31	58	111	3.9e-8	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000162606
AA Change: V181A

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000123866
Gene: ENSMUSG00000019795
AA Change: V181A

Domain	Start	End	E-Value	Type
low complexity region	7	25	N/A	INTRINSIC
Pfam:PCMT	66	279	2e-88	PFAM
Pfam:Ubie_methyltran	126	259	1e-6	PFAM
Pfam:Methyltransf_31	134	283	3.5e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162682

SMART Domains

Protein: ENSMUSP00000124246
Gene: ENSMUSG00000019795

Domain	Start	End	E-Value	Type
Pfam:PCMT	1	66	7.5e-26	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000163085
AA Change: V167A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000125144
Gene: ENSMUSG00000019795
AA Change: V167A

Domain	Start	End	E-Value	Type
transmembrane domain	15	37	N/A	INTRINSIC
Pfam:PCMT	52	265	9.1e-89	PFAM
Pfam:Ubie_methyltran	112	244	3.1e-7	PFAM
Pfam:Methyltransf_31	120	270	9.8e-9	PFAM
Pfam:Methyltransf_18	122	227	2.7e-9	PFAM
Pfam:Methyltransf_11	127	225	1.4e-6	PFAM

Meta Mutation Damage Score

0.8310

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.2%
20x: 95.1%

Validation Efficiency

100% (60/60)

MGI Phenotype

PHENOTYPE: Homozygous disruption of this gene causes accumulation of modified proteins, growth retardation and fatal epileptic seizures. Homozygotes for one null allele also show a small spleen, altered lipid, hormone, mineral and enzyme profiles, kyphosis, enlarged brain and abnormal dendritic arborizations. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579C12Rik	T	C	9: 89,051,041 (GRCm39)		noncoding transcript	Het
Ankfy1	A	T	11: 72,637,757 (GRCm39)	H483L	probably benign	Het
Ankrd46	C	T	15: 36,479,447 (GRCm39)	G215R	probably damaging	Het
Apobec1	T	C	6: 122,558,327 (GRCm39)	I143V	probably benign	Het
Atp2b4	C	A	1: 133,657,610 (GRCm39)	V627F	probably damaging	Het
Ccdc80	T	A	16: 44,947,588 (GRCm39)	Y855*	probably null	Het
Cd209b	T	C	8: 3,975,396 (GRCm39)	E88G	probably damaging	Het
Ceacam14	T	G	7: 17,548,110 (GRCm39)	W67G	probably damaging	Het
Cope	T	C	8: 70,757,306 (GRCm39)	V50A	probably benign	Het
Dcaf13	C	A	15: 38,987,759 (GRCm39)	D168E	probably benign	Het
Dhcr7	T	G	7: 143,391,576 (GRCm39)	M55R	probably damaging	Het
Enpp7	A	T	11: 118,879,634 (GRCm39)	Y96F	probably benign	Het
Esco1	T	C	18: 10,584,327 (GRCm39)	D60G	probably benign	Het
Fgfr3	G	A	5: 33,880,642 (GRCm39)		probably benign	Het
Frzb	T	C	2: 80,248,259 (GRCm39)	D280G	probably damaging	Het
Gcat	A	G	15: 78,920,610 (GRCm39)	I317V	probably benign	Het
Gm13030	A	T	4: 138,600,820 (GRCm39)		probably benign	Het
Gmds	A	G	13: 32,312,024 (GRCm39)	L135P	probably damaging	Het
Htra2	G	A	6: 83,030,995 (GRCm39)	P138L	probably damaging	Het
Il5	A	G	11: 53,614,626 (GRCm39)	N89S	probably damaging	Het
Ints3	G	A	3: 90,315,834 (GRCm39)	T310M	possibly damaging	Het
Itih2	T	C	2: 10,102,804 (GRCm39)	I777V	probably null	Het
Kctd9	T	C	14: 67,977,836 (GRCm39)	L382S	probably damaging	Het
Loricrin	A	G	3: 91,988,789 (GRCm39)	S166P	unknown	Het
Mga	T	A	2: 119,733,810 (GRCm39)	N219K	probably damaging	Het
Mtmr4	A	T	11: 87,501,868 (GRCm39)	R641*	probably null	Het
Muc6	C	T	7: 141,235,078 (GRCm39)	A611T	possibly damaging	Het
Obox3-ps8	A	T	17: 36,763,903 (GRCm39)		noncoding transcript	Het
Or5p54	A	T	7: 107,554,096 (GRCm39)	M83L	probably benign	Het
Otud4	C	T	8: 80,377,671 (GRCm39)	L111F	possibly damaging	Het
Pcdhga12	T	A	18: 37,899,314 (GRCm39)	S49T	possibly damaging	Het
Pcdhgc3	A	G	18: 37,941,549 (GRCm39)	D650G	probably damaging	Het
Pcnt	A	T	10: 76,225,381 (GRCm39)		probably null	Het
Pcx	G	T	19: 4,652,504 (GRCm39)	V164F	probably damaging	Het
Plekhg4	T	C	8: 106,102,745 (GRCm39)		probably null	Het
Pmch	A	G	10: 87,927,707 (GRCm39)	E136G	probably damaging	Het
Prkar1a	A	G	11: 109,550,886 (GRCm39)	D80G	probably benign	Het
Ryr3	T	C	2: 112,560,647 (GRCm39)		probably null	Het
Slc10a7	T	C	8: 79,413,253 (GRCm39)	S171P	possibly damaging	Het
Sox6	A	T	7: 115,301,008 (GRCm39)	M153K	possibly damaging	Het
Srgap2	T	C	1: 131,217,475 (GRCm39)	I946V	probably benign	Het
Strbp	T	C	2: 37,535,495 (GRCm39)	E71G	probably benign	Het
Synpo2l	C	A	14: 20,712,360 (GRCm39)	A87S	probably damaging	Het
Tnrc18	T	C	5: 142,757,446 (GRCm39)	D1025G	unknown	Het
Tnxb	A	G	17: 34,928,599 (GRCm39)	H2671R	possibly damaging	Het
Tor1b	GGACG	GG	2: 30,846,957 (GRCm39)		probably benign	Het
Umodl1	A	T	17: 31,205,439 (GRCm39)	D649V	possibly damaging	Het
Usp13	G	T	3: 32,959,585 (GRCm39)	A559S	probably damaging	Het
Vps45	G	A	3: 95,926,969 (GRCm39)	P526L	probably benign	Het
Zfp687	A	G	3: 94,916,457 (GRCm39)	V855A	probably damaging	Het
Zfp771	T	A	7: 126,853,448 (GRCm39)	C205S	probably damaging	Het

Other mutations in Pcmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02934:Pcmt1	APN	10	7,516,491 (GRCm39)	missense	probably benign	0.00
R1968:Pcmt1	UTSW	10	7,516,474 (GRCm39)	nonsense	probably null
R3889:Pcmt1	UTSW	10	7,524,814 (GRCm39)	critical splice donor site	probably null
R5630:Pcmt1	UTSW	10	7,524,857 (GRCm39)	missense	probably damaging	1.00
R5705:Pcmt1	UTSW	10	7,513,954 (GRCm39)	missense	possibly damaging	0.86
R6667:Pcmt1	UTSW	10	7,538,913 (GRCm39)	missense	probably damaging	1.00
R7163:Pcmt1	UTSW	10	7,513,922 (GRCm39)	missense	probably benign	0.01
R7168:Pcmt1	UTSW	10	7,513,946 (GRCm39)	missense	probably damaging	1.00
R7531:Pcmt1	UTSW	10	7,556,369 (GRCm39)	splice site	probably null
R8012:Pcmt1	UTSW	10	7,516,527 (GRCm39)	missense	probably benign	0.26
R8435:Pcmt1	UTSW	10	7,515,825 (GRCm39)	missense	possibly damaging	0.94
R9134:Pcmt1	UTSW	10	7,520,207 (GRCm39)	splice site	probably benign
R9140:Pcmt1	UTSW	10	7,514,678 (GRCm39)	makesense	probably null
R9595:Pcmt1	UTSW	10	7,524,817 (GRCm39)	missense	possibly damaging	0.52

Predicted Primers

PCR Primer
(F):5'- TCCGCTGAAATGGATGAGGG -3'
(R):5'- ACATGGACAGTTGTAAACAGTCAG -3'

Sequencing Primer
(F):5'- CTGAAATGGATGAGGGCTGCTG -3'
(R):5'- TTAGCCCTGTGGACTCTT -3'

Posted On

2016-10-06