Mutagenetix > Incidental Mutation

Incidental Mutation 'R4660:Pgs1'

352791

Institutional Source

Beutler Lab

Gene Symbol

Pgs1

Ensembl Gene

ENSMUSG00000017715

Gene Name

phosphatidylglycerophosphate synthase 1

Synonyms

2610019F11Rik, 4933424M23Rik

MMRRC Submission

041920-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4660 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

117877118-117914837 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 117910503 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 538 (V538A)

Ref Sequence

ENSEMBL: ENSMUSP00000121973 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000084803] [ENSMUST00000100185] [ENSMUST00000106308] [ENSMUST00000132676] [ENSMUST00000132685]

AlphaFold

Q8BHF7

Predicted Effect

probably benign
Transcript: ENSMUST00000017859

SMART Domains

Protein: ENSMUSP00000017859
Gene: ENSMUSG00000017715

Domain	Start	End	E-Value	Type
low complexity region	11	56	N/A	INTRINSIC
SCOP:d1f0ia1	70	287	4e-25	SMART
PDB:3HSI\|C	81	464	7e-8	PDB
Blast:PLDc	211	237	2e-8	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000084803

SMART Domains

Protein: ENSMUSP00000081864
Gene: ENSMUSG00000033987

Domain	Start	End	E-Value	Type
Pfam:DHC_N1	183	766	8.5e-142	PFAM
low complexity region	1015	1028	N/A	INTRINSIC
Pfam:DHC_N2	1260	1673	5.8e-135	PFAM
Pfam:AAA_6	1793	2023	6e-161	PFAM
low complexity region	2092	2104	N/A	INTRINSIC
Pfam:AAA_5	2107	2243	7.8e-13	PFAM
Pfam:AAA_7	2400	2671	1.1e-171	PFAM
Pfam:AAA_8	2748	3015	4.9e-166	PFAM
Pfam:MT	3027	3370	3.4e-214	PFAM
Pfam:AAA_9	3388	3615	2.4e-144	PFAM
Pfam:Dynein_heavy	3742	4452	N/A	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000100185

SMART Domains

Protein: ENSMUSP00000097760
Gene: ENSMUSG00000017715

Domain	Start	End	E-Value	Type
SCOP:d1f0ia1	18	158	7e-13	SMART
Blast:PLDc	82	108	1e-8	BLAST
low complexity region	202	215	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106308

SMART Domains

Protein: ENSMUSP00000101915
Gene: ENSMUSG00000033987

Domain	Start	End	E-Value	Type
Pfam:DHC_N1	184	764	1.7e-152	PFAM
low complexity region	1015	1028	N/A	INTRINSIC
Pfam:DHC_N2	1262	1671	4.1e-132	PFAM
Pfam:AAA_6	1793	2023	7e-149	PFAM
low complexity region	2092	2104	N/A	INTRINSIC
Pfam:AAA_5	2107	2243	2.5e-11	PFAM
Pfam:AAA_7	2400	2671	4.4e-169	PFAM
Pfam:AAA_8	2748	3015	7.1e-163	PFAM
Pfam:MT	3027	3370	1.1e-210	PFAM
Pfam:AAA_9	3392	3614	1e-84	PFAM
Pfam:Dynein_heavy	3748	4479	3.5e-230	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000132676
AA Change: V538A

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000121973
Gene: ENSMUSG00000017715
AA Change: V538A

Domain	Start	End	E-Value	Type
low complexity region	12	57	N/A	INTRINSIC
SCOP:d1f0ia1	71	288	3e-25	SMART
PDB:3HSI\|C	82	475	3e-9	PDB
Blast:PLDc	212	238	2e-8	BLAST
Blast:PLDc	459	490	1e-13	BLAST
low complexity region	508	521	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000132685

SMART Domains

Protein: ENSMUSP00000120542
Gene: ENSMUSG00000033987

Domain	Start	End	E-Value	Type
Pfam:DHC_N2	279	688	3.1e-132	PFAM
Pfam:AAA_6	811	1041	5.3e-149	PFAM
low complexity region	1110	1122	N/A	INTRINSIC
Blast:AAA	1123	1354	1e-104	BLAST
Pfam:AAA_7	1452	1671	8.9e-134	PFAM
Pfam:AAA_8	1763	2030	5.4e-163	PFAM
Pfam:MT	2042	2168	6.8e-52	PFAM
Pfam:MT	2163	2412	8.2e-149	PFAM
Pfam:AAA_9	2434	2656	7.9e-85	PFAM
Pfam:Dynein_heavy	2790	3457	2.6e-209	PFAM
Pfam:Dynein_heavy	3460	3569	4.6e-17	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155507

Meta Mutation Damage Score

0.2282

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 95.0%

Validation Efficiency

96% (102/106)

Allele List at MGI

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adra1d	T	C	2: 131,403,062 (GRCm39)	T343A	probably damaging	Het
Angptl4	A	T	17: 33,996,249 (GRCm39)		probably benign	Het
Antxr2	A	T	5: 98,151,913 (GRCm39)		probably null	Het
Ap1b1	T	A	11: 4,966,760 (GRCm39)	V145E	probably damaging	Het
Asns	G	T	6: 7,678,012 (GRCm39)	N355K	probably benign	Het
Asxl3	A	G	18: 22,649,534 (GRCm39)	T508A	probably benign	Het
B4galt7	T	A	13: 55,752,111 (GRCm39)	V54D	possibly damaging	Het
Bach2	C	T	4: 32,562,777 (GRCm39)	P415S	probably benign	Het
Bbs9	G	A	9: 22,490,063 (GRCm39)	R278Q	probably benign	Het
Blzf1	C	T	1: 164,134,062 (GRCm39)		probably benign	Het
Btd	A	T	14: 31,389,760 (GRCm39)	T494S	probably benign	Het
Casp9	C	T	4: 141,540,934 (GRCm39)	T434I	probably benign	Het
Cavin2	T	C	1: 51,340,510 (GRCm39)	S396P	probably benign	Het
Ccnk	C	T	12: 108,168,575 (GRCm39)		probably benign	Het
Cldn8	G	A	16: 88,359,296 (GRCm39)	H210Y	probably benign	Het
Clip1	G	A	5: 123,717,437 (GRCm39)	T1284I	probably damaging	Het
Coch	T	C	12: 51,642,268 (GRCm39)	V80A	probably benign	Het
Cttnbp2	A	G	6: 18,406,536 (GRCm39)	S1052P	probably benign	Het
Cyp2j7	C	T	4: 96,083,579 (GRCm39)	R457K	probably benign	Het
Dalrd3	T	C	9: 108,447,568 (GRCm39)	S129P	probably benign	Het
Ddx10	A	G	9: 53,147,698 (GRCm39)		probably null	Het
Dnah7b	A	T	1: 46,328,696 (GRCm39)	T3143S	probably damaging	Het
Dynlt1b	A	G	17: 6,699,279 (GRCm39)	T10A	probably benign	Het
Eif2s2	G	A	2: 154,730,189 (GRCm39)	T36I	probably benign	Het
Fam118b	A	T	9: 35,146,551 (GRCm39)	H105Q	possibly damaging	Het
Galntl5	T	A	5: 25,408,377 (GRCm39)	I250N	probably damaging	Het
Gm11544	C	T	11: 94,736,306 (GRCm39)		noncoding transcript	Het
Gm5709	C	T	3: 59,526,124 (GRCm39)		noncoding transcript	Het
Golgb1	T	A	16: 36,707,980 (GRCm39)	I107N	probably damaging	Het
Gpld1	T	C	13: 25,166,586 (GRCm39)		probably null	Het
Grik1	T	A	16: 87,720,019 (GRCm39)	T768S	probably damaging	Het
H2-T23	T	G	17: 36,341,108 (GRCm39)	Q349P	probably damaging	Het
Ing3	A	T	6: 21,973,710 (GRCm39)		probably benign	Het
Iqgap3	T	G	3: 88,027,483 (GRCm39)	L702R	probably damaging	Het
Itga8	A	G	2: 12,270,069 (GRCm39)	V139A	probably damaging	Het
Jam2	G	A	16: 84,609,840 (GRCm39)	V151M	probably damaging	Het
Kbtbd12	T	C	6: 88,594,772 (GRCm39)	I353V	probably benign	Het
Kif27	T	C	13: 58,471,730 (GRCm39)	E786G	probably damaging	Het
Lingo4	T	A	3: 94,310,672 (GRCm39)	S537T	probably benign	Het
Lipo3	C	T	19: 33,598,360 (GRCm39)		probably benign	Het
Lrrc3	G	T	10: 77,729,866 (GRCm39)		probably benign	Het
Ltbp3	T	A	19: 5,798,814 (GRCm39)		probably null	Het
Lyg1	T	A	1: 37,985,942 (GRCm39)		probably benign	Het
Mcm9	T	C	10: 53,424,623 (GRCm39)	I656V	probably benign	Het
Mfsd8	T	A	3: 40,776,372 (GRCm39)	I427F	probably benign	Het
Mga	T	A	2: 119,769,104 (GRCm39)		probably benign	Het
Miga1	A	G	3: 151,993,155 (GRCm39)	L422P	probably damaging	Het
Msantd3	A	G	4: 48,552,536 (GRCm39)	I42V	probably benign	Het
Mybbp1a	T	C	11: 72,336,538 (GRCm39)	V510A	probably benign	Het
Nccrp1	G	T	7: 28,245,760 (GRCm39)	P135T	probably damaging	Het
Neb	T	A	2: 52,145,600 (GRCm39)	M2975L	possibly damaging	Het
Nfxl1	A	T	5: 72,710,011 (GRCm39)	I171N	probably damaging	Het
Odad2	A	G	18: 7,211,609 (GRCm39)	V755A	possibly damaging	Het
Or10q3	T	C	19: 11,848,412 (GRCm39)	H56R	possibly damaging	Het
Or12j5	A	T	7: 140,083,933 (GRCm39)	F146L	probably benign	Het
Or13a19	T	C	7: 139,903,325 (GRCm39)	F238L	possibly damaging	Het
Otop1	T	G	5: 38,457,368 (GRCm39)	S376A	possibly damaging	Het
Pdgfra	T	C	5: 75,322,932 (GRCm39)	V10A	possibly damaging	Het
Ppa2	A	T	3: 133,032,445 (GRCm39)	T97S	probably damaging	Het
Pramel22	T	A	4: 143,380,847 (GRCm39)	Y392F	probably benign	Het
Pramel26	A	G	4: 143,538,435 (GRCm39)	S179P	probably benign	Het
Prdm10	G	A	9: 31,238,624 (GRCm39)	C172Y	probably damaging	Het
Prrc2c	G	A	1: 162,508,464 (GRCm39)	P1091L	probably damaging	Het
Pthlh	G	A	6: 147,158,796 (GRCm39)	R55C	probably damaging	Het
Ptpn9	A	T	9: 56,943,782 (GRCm39)	T105S	probably benign	Het
Rundc1	T	A	11: 101,324,830 (GRCm39)	V512E	possibly damaging	Het
Scrib	G	A	15: 75,937,185 (GRCm39)	S307L	probably damaging	Het
Sec23ip	A	G	7: 128,352,010 (GRCm39)	S26G	probably null	Het
Sec61a2	A	G	2: 5,878,504 (GRCm39)		probably benign	Het
Sema3c	T	C	5: 17,877,511 (GRCm39)	V206A	probably damaging	Het
Sgk2	C	T	2: 162,839,763 (GRCm39)	H124Y	possibly damaging	Het
Slc26a6	C	T	9: 108,738,540 (GRCm39)	T592I	probably damaging	Het
Slc5a11	T	C	7: 122,864,486 (GRCm39)	Y361H	probably damaging	Het
Smc6	T	C	12: 11,324,008 (GRCm39)	V51A	probably damaging	Het
Stab1	A	T	14: 30,876,872 (GRCm39)	N817K	possibly damaging	Het
Swt1	A	T	1: 151,283,348 (GRCm39)	D336E	probably benign	Het
Taf13	T	A	3: 108,480,293 (GRCm39)		probably benign	Het
Tmub2	T	C	11: 102,175,845 (GRCm39)		probably benign	Het
Tnf	A	G	17: 35,419,156 (GRCm39)	S209P	probably benign	Het
Try10	A	G	6: 41,334,761 (GRCm39)	Y229C	probably damaging	Het
Ttbk1	G	T	17: 46,788,714 (GRCm39)	Y183*	probably null	Het
Ttc17	A	T	2: 94,194,774 (GRCm39)	I533N	possibly damaging	Het
Tubb6	C	T	18: 67,535,016 (GRCm39)	P305L	probably damaging	Het
Tulp3	G	A	6: 128,300,017 (GRCm39)		probably benign	Het
Usp9x	A	G	X: 12,989,747 (GRCm39)	R776G	possibly damaging	Het
Virma	T	C	4: 11,513,505 (GRCm39)	V453A	probably damaging	Het
Vmn2r103	A	T	17: 20,032,077 (GRCm39)	N617I	probably damaging	Het
Xirp1	G	T	9: 119,846,058 (GRCm39)	L942M	probably damaging	Het
Zc3h7b	T	G	15: 81,676,451 (GRCm39)	V731G	probably benign	Het
Zfp534	C	T	4: 147,759,175 (GRCm39)	G498D	probably benign	Het
Zfp639	T	C	3: 32,574,679 (GRCm39)	Y435H	probably damaging	Het
Zxdc	A	G	6: 90,355,820 (GRCm39)	H443R	probably damaging	Het

Other mutations in Pgs1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00943:Pgs1	APN	11	117,896,366 (GRCm39)	missense	probably benign	0.07
R1703:Pgs1	UTSW	11	117,905,554 (GRCm39)	splice site	probably benign
R1747:Pgs1	UTSW	11	117,892,457 (GRCm39)	missense	probably benign	0.15
R1938:Pgs1	UTSW	11	117,896,553 (GRCm39)	missense	probably damaging	1.00
R2023:Pgs1	UTSW	11	117,893,228 (GRCm39)	missense	probably benign	0.00
R2066:Pgs1	UTSW	11	117,905,396 (GRCm39)	splice site	probably benign
R3826:Pgs1	UTSW	11	117,910,584 (GRCm39)	splice site	probably null
R3915:Pgs1	UTSW	11	117,910,472 (GRCm39)	missense	probably benign
R4201:Pgs1	UTSW	11	117,893,362 (GRCm39)	missense	probably damaging	1.00
R4668:Pgs1	UTSW	11	117,894,333 (GRCm39)	missense	probably damaging	0.99
R4718:Pgs1	UTSW	11	117,896,709 (GRCm39)	missense	probably damaging	1.00
R4972:Pgs1	UTSW	11	117,896,719 (GRCm39)	critical splice donor site	probably null
R4974:Pgs1	UTSW	11	117,896,345 (GRCm39)	missense	probably benign	0.00
R5414:Pgs1	UTSW	11	117,905,502 (GRCm39)	missense	probably damaging	0.98
R6053:Pgs1	UTSW	11	117,892,535 (GRCm39)	missense	probably damaging	1.00
R6382:Pgs1	UTSW	11	117,894,186 (GRCm39)	missense	probably damaging	1.00
R7030:Pgs1	UTSW	11	117,893,312 (GRCm39)	missense	probably damaging	0.99
R9777:Pgs1	UTSW	11	117,894,256 (GRCm39)	missense	probably benign	0.00
Z1177:Pgs1	UTSW	11	117,896,382 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCTAAATCAGCGATATACAGAGGC -3'
(R):5'- GAGCAAAGTCCAGCGCTTAC -3'

Sequencing Primer
(F):5'- CTCTTGGCTGGGGTCCTCAG -3'
(R):5'- AGTCCAGCGCTTACTTTAAAACTGC -3'

Posted On

2015-10-08