Mutagenetix > Incidental Mutation

Incidental Mutation 'R6667:Pcmt1'

527028

Institutional Source

Beutler Lab

Gene Symbol

Pcmt1

Ensembl Gene

ENSMUSG00000019795

Gene Name

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

Synonyms

PIMT, protein carboxyl methyltransferase

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.114) question?

Stock #

R6667 (G1)

Quality Score

224.009

Status

Validated

Chromosome

Chromosomal Location

7629373-7681136 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 7663149 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 38 (L38P)

Ref Sequence

ENSEMBL: ENSMUSP00000125144 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040135] [ENSMUST00000159917] [ENSMUST00000159977] [ENSMUST00000161123] [ENSMUST00000162606] [ENSMUST00000162682] [ENSMUST00000163085]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000040135

SMART Domains

Protein: ENSMUSP00000046732
Gene: ENSMUSG00000040034

Domain	Start	End	E-Value	Type
Blast:WD40	1	48	1e-15	BLAST
WD40	64	101	3.57e0	SMART
WD40	124	157	2.45e2	SMART
WD40	160	199	9.55e0	SMART
WD40	206	246	2.15e-4	SMART
WD40	250	290	2.19e-5	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000159917
AA Change: L52P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000124932
Gene: ENSMUSG00000019795
AA Change: L52P

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

probably benign
Transcript: ENSMUST00000159977

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160250

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160517

Predicted Effect

probably benign
Transcript: ENSMUST00000161123
AA Change: L39P

PolyPhen 2 Score 0.076 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000124100
Gene: ENSMUSG00000019795
AA Change: L39P

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162346

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162527

Predicted Effect

probably damaging
Transcript: ENSMUST00000162606
AA Change: L52P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000123866
Gene: ENSMUSG00000019795
AA Change: L52P

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: L38P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000125144
Gene: ENSMUSG00000019795
AA Change: L38P

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

0.2191

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.6%

Validation Efficiency

98% (41/42)

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: 44 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3100002H09Rik	G	T	4: 124,610,642	A39E	probably damaging	Het
Agtr1b	T	A	3: 20,315,749	N231I	possibly damaging	Het
Alpk2	T	C	18: 65,307,740	E661G	probably damaging	Het
Ankrd26	C	T	6: 118,507,788	S1496N	probably benign	Het
Asah2	T	C	19: 31,995,358	N659S	probably benign	Het
Atp12a	T	C	14: 56,384,188	V760A	possibly damaging	Het
Casp2	T	C	6: 42,279,836	C343R	probably damaging	Het
Cblb	T	A	16: 52,152,644	M446K	possibly damaging	Het
Cipc	T	C	12: 86,962,090	V241A	probably benign	Het
Ddit4l	A	G	3: 137,626,121	K83E	probably benign	Het
E430018J23Rik	A	G	7: 127,393,423	M5T	probably benign	Het
Epc2	A	G	2: 49,522,669	T220A	probably damaging	Het
Epha5	T	C	5: 84,071,191	D741G	probably damaging	Het
Flg2	A	T	3: 93,201,761	R365S	possibly damaging	Het
Ggn	A	T	7: 29,172,668	H491L	possibly damaging	Het
Gm21119	T	C	8: 20,621,939	S267P	probably benign	Het
Gm8332	A	T	12: 88,249,705	D132E	unknown	Het
Gpat2	G	C	2: 127,431,918	G294R	possibly damaging	Het
Ighv6-4	A	G	12: 114,406,532	V100A	probably benign	Het
Invs	A	T	4: 48,402,870	Y501F	possibly damaging	Het
Iqcm	G	T	8: 75,753,352	G313W	probably damaging	Het
Jph2	A	G	2: 163,376,286	S157P	probably damaging	Het
Mast4	T	C	13: 102,737,496	E1596G	probably damaging	Het
Mllt6	T	A	11: 97,676,934	L759Q	probably damaging	Het
Nalcn	A	G	14: 123,321,323	L837P	probably damaging	Het
Neb	G	A	2: 52,147,189	T6836I	probably damaging	Het
Nol12	T	A	15: 78,940,080	D133E	probably benign	Het
Olfr1136	A	G	2: 87,693,570	V104A	probably benign	Het
Oxtr	C	A	6: 112,477,099		probably benign	Het
Pik3r2	T	C	8: 70,769,173	Y617C	probably damaging	Het
Prl7a2	T	C	13: 27,661,041	N121D	probably benign	Het
Pvr	G	T	7: 19,905,802	Q380K	probably benign	Het
Rtn2	A	G	7: 19,287,259	E188G	probably benign	Het
Setd4	C	A	16: 93,590,030	R260L	probably benign	Het
Six5	A	G	7: 19,096,569	N374D	probably benign	Het
Slc9b1	T	C	3: 135,371,965	I140T	probably damaging	Het
Supt16	A	G	14: 52,172,063	F797L	probably damaging	Het
Tbata	T	C	10: 61,185,363	L262P	probably damaging	Het
Tti1	A	T	2: 158,008,427	C297*	probably null	Het
Ush1c	C	A	7: 46,225,624	G139C	probably damaging	Het
Vmn1r1	C	T	1: 182,157,777	V108I	probably benign	Het
Vmn2r116	C	T	17: 23,401,092	T600I	probably damaging	Het
Zfp873	A	G	10: 82,060,589	T422A	probably benign	Het
Zfp943	G	A	17: 21,992,908	C325Y	probably damaging	Het

Other mutations in Pcmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02934:Pcmt1	APN	10	7640727	missense	probably benign	0.00
R1968:Pcmt1	UTSW	10	7640710	nonsense	probably null
R3889:Pcmt1	UTSW	10	7649050	critical splice donor site	probably null
R5454:Pcmt1	UTSW	10	7640745	missense	probably damaging	1.00
R5630:Pcmt1	UTSW	10	7649093	missense	probably damaging	1.00
R5705:Pcmt1	UTSW	10	7638190	missense	possibly damaging	0.86
R7163:Pcmt1	UTSW	10	7638158	missense	probably benign	0.01
R7168:Pcmt1	UTSW	10	7638182	missense	probably damaging	1.00
R7531:Pcmt1	UTSW	10	7680605	splice site	probably null
R8012:Pcmt1	UTSW	10	7640763	missense	probably benign	0.26
R8435:Pcmt1	UTSW	10	7640061	missense	possibly damaging	0.94
R9134:Pcmt1	UTSW	10	7644443	splice site	probably benign
R9140:Pcmt1	UTSW	10	7638914	makesense	probably null
R9595:Pcmt1	UTSW	10	7649053	missense	possibly damaging	0.52

Predicted Primers

PCR Primer
(F):5'- TGCTAGTCCAGTCACCAGAAAC -3'
(R):5'- AACTGAGCAGCGTTCGTTTG -3'

Sequencing Primer
(F):5'- TCCACATCGCCGAGTGACAG -3'
(R):5'- ACCGAGCACTGGTTATCGC -3'

Posted On

2018-07-23