Mutagenetix > Incidental Mutation

Incidental Mutation 'R9096:Pld3'

691358

Institutional Source

Beutler Lab

Gene Symbol

Pld3

Ensembl Gene

ENSMUSG00000003363

Gene Name

phospholipase D family member 3

Synonyms

Sam-9

MMRRC Submission

068911-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9096 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

27231425-27252643 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 27232089 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 397 (V397A)

Ref Sequence

ENSEMBL: ENSMUSP00000113820 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000037134] [ENSMUST00000108353] [ENSMUST00000117095] [ENSMUST00000117611]

AlphaFold

O35405

Predicted Effect

probably benign
Transcript: ENSMUST00000037134

SMART Domains

Protein: ENSMUSP00000043175
Gene: ENSMUSG00000040424

Domain	Start	End	E-Value	Type
SCOP:d1howa_	1	142	8e-12	SMART
Blast:S_TKc	1	143	8e-99	BLAST
PDB:3ANR\|D	1	155	1e-12	PDB
low complexity region	192	206	N/A	INTRINSIC
low complexity region	389	399	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108353

SMART Domains

Protein: ENSMUSP00000103990
Gene: ENSMUSG00000040424

Domain	Start	End	E-Value	Type
S_TKc	11	347	9.31e-74	SMART
low complexity region	396	410	N/A	INTRINSIC
low complexity region	593	603	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000117095
AA Change: V397A

PolyPhen 2 Score 0.081 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000113820
Gene: ENSMUSG00000003363
AA Change: V397A

Domain	Start	End	E-Value	Type
low complexity region	25	36	N/A	INTRINSIC
transmembrane domain	38	60	N/A	INTRINSIC
PLDc	194	221	9.25e-10	SMART
Pfam:PLDc_3	224	401	1.6e-43	PFAM
PLDc	409	435	1.19e-3	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000117611
AA Change: V397A

PolyPhen 2 Score 0.081 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000112942
Gene: ENSMUSG00000003363
AA Change: V397A

Domain	Start	End	E-Value	Type
low complexity region	25	36	N/A	INTRINSIC
transmembrane domain	38	60	N/A	INTRINSIC
PLDc	194	221	9.25e-10	SMART
low complexity region	285	297	N/A	INTRINSIC
PLDc	409	435	1.19e-3	SMART

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

98% (57/58)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the phospholipase D (PLD) family of enzymes that catalyze the hydrolysis of membrane phospholipids. The encoded protein is a single-pass type II membrane protein and contains two PLD phosphodiesterase domains. This protein influences processing of amyloid-beta precursor protein. Mutations in this gene are associated with Alzheimer disease risk. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2014]

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900026A02Rik	A	T	5: 113,339,793 (GRCm39)	V73E		Het
Abhd12b	T	A	12: 70,210,207 (GRCm39)	Y128N	probably damaging	Het
Arhgap40	A	T	2: 158,389,584 (GRCm39)	M586L	probably benign	Het
Armt1	T	C	10: 4,384,829 (GRCm39)	S15P	probably damaging	Het
Arnt	G	T	3: 95,397,588 (GRCm39)	S535I	probably benign	Het
Bmper	T	C	9: 23,134,988 (GRCm39)	S18P	possibly damaging	Het
Catsperg1	G	C	7: 28,884,152 (GRCm39)	T987R	probably damaging	Het
Col9a1	A	T	1: 24,224,207 (GRCm39)	I130F	unknown	Het
Dennd1a	G	T	2: 37,690,077 (GRCm39)	L1008I	probably damaging	Het
Depdc1a	T	A	3: 159,204,117 (GRCm39)	D55E	probably benign	Het
Dlc1	A	T	8: 37,080,721 (GRCm39)	I10N	probably benign	Het
Dnah1	T	A	14: 30,983,027 (GRCm39)	I4203F	probably damaging	Het
Dzank1	G	T	2: 144,316,882 (GRCm39)	L767I	possibly damaging	Het
Eprs1	C	A	1: 185,139,303 (GRCm39)	A896E	probably benign	Het
Fryl	T	C	5: 73,265,920 (GRCm39)	D467G	probably benign	Het
Gab3	TTC	TTCCTC	X: 74,043,610 (GRCm39)		probably benign	Het
Gimd1	T	A	3: 132,340,661 (GRCm39)	M59K	probably benign	Het
Gm3667	T	C	14: 18,270,388 (GRCm39)	Y139C	probably damaging	Het
Gng2	T	A	14: 19,941,471 (GRCm39)		probably null	Het
Gpr162	A	G	6: 124,836,570 (GRCm39)	I367T	probably benign	Het
Hacd4	A	G	4: 88,355,695 (GRCm39)		probably null	Het
Hmcn1	C	T	1: 150,532,869 (GRCm39)	V3105M	probably benign	Het
Iws1	T	C	18: 32,216,373 (GRCm39)	V371A	probably benign	Het
Kctd10	C	T	5: 114,508,232 (GRCm39)	R92Q	probably damaging	Het
Lepr	T	C	4: 101,631,418 (GRCm39)	F643L	possibly damaging	Het
Lpgat1	T	C	1: 191,451,569 (GRCm39)	V65A	possibly damaging	Het
Lrrk2	C	T	15: 91,557,459 (GRCm39)		probably benign	Het
Magel2	A	G	7: 62,030,297 (GRCm39)	D1067G	unknown	Het
Mrc2	A	G	11: 105,231,398 (GRCm39)	D777G	probably damaging	Het
Nol10	T	A	12: 17,466,199 (GRCm39)	D531E	probably benign	Het
Odf2	T	A	2: 29,783,508 (GRCm39)	V103D	probably damaging	Het
Or4f7	T	A	2: 111,644,196 (GRCm39)	K292*	probably null	Het
Pcdhb21	A	G	18: 37,648,071 (GRCm39)	Y400C	probably damaging	Het
Pkn2	C	T	3: 142,515,249 (GRCm39)	R695Q	probably benign	Het
Ppp1r9a	A	G	6: 4,906,012 (GRCm39)	D189G	probably damaging	Het
Ppp2r1b	A	G	9: 50,777,856 (GRCm39)	K267R	probably benign	Het
Prkca	A	G	11: 107,905,061 (GRCm39)	S226P	probably benign	Het
Ptpru	T	C	4: 131,499,843 (GRCm39)	N1267S	probably damaging	Het
Pxn	T	A	5: 115,686,680 (GRCm39)	C391S	probably benign	Het
Rars1	T	C	11: 35,718,256 (GRCm39)	E136G	probably benign	Het
Rrp12	A	T	19: 41,878,577 (GRCm39)	D189E	probably benign	Het
Rsf1	GCG	GCGACGGCGCCG	7: 97,229,114 (GRCm39)		probably benign	Het
Sdc1	T	C	12: 8,841,665 (GRCm39)	L265P	probably damaging	Het
Sycp2l	A	T	13: 41,300,070 (GRCm39)	D428V	possibly damaging	Het
Tasp1	A	T	2: 139,725,690 (GRCm39)		probably null	Het
Telo2	T	C	17: 25,324,066 (GRCm39)	T550A	probably benign	Het
Tmem131l	A	T	3: 83,850,122 (GRCm39)	N225K	probably damaging	Het
Tmem260	T	A	14: 48,757,803 (GRCm39)	V706D	unknown	Het
Tnr	T	A	1: 159,677,804 (GRCm39)	M63K	probably benign	Het
Ttn	A	G	2: 76,572,413 (GRCm39)	I26160T	probably damaging	Het
Ubap1	T	C	4: 41,379,872 (GRCm39)		probably null	Het
Ush2a	C	T	1: 188,198,333 (GRCm39)	P1466S	probably benign	Het
Usp24	T	G	4: 106,254,508 (GRCm39)	M1495R	probably benign	Het
Utp20	T	C	10: 88,611,180 (GRCm39)	N1379S	probably damaging	Het
Vmn1r16	A	T	6: 57,300,250 (GRCm39)	I124N	probably benign	Het
Vmn1r181	A	G	7: 23,684,444 (GRCm39)	N303S	probably benign	Het
Vmn1r50	G	A	6: 90,085,022 (GRCm39)	V256I	probably benign	Het
Vps54	A	G	11: 21,227,913 (GRCm39)	N288S	possibly damaging	Het
Zfp266	A	T	9: 20,416,440 (GRCm39)	F50Y	probably damaging	Het

Other mutations in Pld3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01474:Pld3	APN	7	27,232,044 (GRCm39)	missense	probably damaging	1.00
R0624:Pld3	UTSW	7	27,239,000 (GRCm39)	missense	possibly damaging	0.94
R1384:Pld3	UTSW	7	27,237,082 (GRCm39)	missense	probably benign	0.00
R1845:Pld3	UTSW	7	27,238,877 (GRCm39)	missense	probably benign	0.01
R2235:Pld3	UTSW	7	27,240,532 (GRCm39)	missense	probably benign	0.00
R3106:Pld3	UTSW	7	27,235,212 (GRCm39)	critical splice donor site	probably null
R5141:Pld3	UTSW	7	27,233,220 (GRCm39)	missense	probably damaging	1.00
R5486:Pld3	UTSW	7	27,233,156 (GRCm39)	missense	probably damaging	0.99
R5518:Pld3	UTSW	7	27,231,796 (GRCm39)	missense	probably damaging	1.00
R5868:Pld3	UTSW	7	27,237,093 (GRCm39)	missense	probably benign	0.00
R6446:Pld3	UTSW	7	27,237,156 (GRCm39)	missense	probably damaging	1.00
R6591:Pld3	UTSW	7	27,231,741 (GRCm39)	missense	probably benign	0.00
R6691:Pld3	UTSW	7	27,231,741 (GRCm39)	missense	probably benign	0.00
R6823:Pld3	UTSW	7	27,235,322 (GRCm39)	missense	probably damaging	1.00
R7162:Pld3	UTSW	7	27,231,899 (GRCm39)	missense	probably damaging	1.00
R8150:Pld3	UTSW	7	27,232,086 (GRCm39)	missense	probably damaging	1.00
R8725:Pld3	UTSW	7	27,239,079 (GRCm39)	nonsense	probably null
R8795:Pld3	UTSW	7	27,235,286 (GRCm39)	missense	possibly damaging	0.52
R9049:Pld3	UTSW	7	27,235,293 (GRCm39)	missense	possibly damaging	0.71
R9292:Pld3	UTSW	7	27,238,879 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- CTTCCAGACCAGTTGGAGGTTC -3'
(R):5'- ATAAGAGCCGTTGCAGCAGG -3'

Sequencing Primer
(F):5'- TTCCTGGGAGCAAGGGG -3'
(R):5'- TTGCAGCAGGTCTGGATCCTC -3'

Posted On

2021-12-30