Mutagenetix > Incidental Mutation

Incidental Mutation 'R5518:Pld3'

431401

Institutional Source

Beutler Lab

Gene Symbol

Pld3

Ensembl Gene

ENSMUSG00000003363

Gene Name

phospholipase D family member 3

Synonyms

Sam-9

MMRRC Submission

043077-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5518 (G1)

Quality Score

188

Status

Validated

Chromosome

Chromosomal Location

27231425-27252643 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 27231796 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 465 (D465G)

Ref Sequence

ENSEMBL: ENSMUSP00000112942 (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 damaging
Transcript: ENSMUST00000117095
AA Change: D465G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000113820
Gene: ENSMUSG00000003363
AA Change: D465G

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 damaging
Transcript: ENSMUST00000117611
AA Change: D465G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000112942
Gene: ENSMUSG00000003363
AA Change: D465G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142981

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155287

Meta Mutation Damage Score

0.9094

Coding Region Coverage

1x: 99.0%
3x: 97.4%
10x: 94.2%
20x: 86.3%

Validation Efficiency

100% (75/75)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc8	C	T	7: 45,769,873 (GRCm39)	E881K	probably benign	Het
Abcf1	C	T	17: 36,269,233 (GRCm39)	R675K	possibly damaging	Het
Abl1	T	A	2: 31,680,754 (GRCm39)	C349S	probably damaging	Het
Acot11	C	A	4: 106,607,207 (GRCm39)	V459L	probably benign	Het
Ank2	A	T	3: 126,753,348 (GRCm39)	V311D	probably damaging	Het
Ankrd11	C	G	8: 123,617,733 (GRCm39)	E2040Q	possibly damaging	Het
Ankrd26	T	C	6: 118,525,869 (GRCm39)	I359V	probably benign	Het
Armc3	T	G	2: 19,302,739 (GRCm39)	L684V	probably benign	Het
Asb10	G	A	5: 24,744,643 (GRCm39)	P184S	probably damaging	Het
Atp10b	T	C	11: 43,042,463 (GRCm39)	S8P	possibly damaging	Het
Blk	G	T	14: 63,615,956 (GRCm39)	S324R	possibly damaging	Het
C4b	G	C	17: 34,953,416 (GRCm39)	N1022K	probably benign	Het
Card6	G	T	15: 5,134,696 (GRCm39)	T169K	probably damaging	Het
Catsper2	T	C	2: 121,236,844 (GRCm39)	T268A	possibly damaging	Het
Cbx3	C	T	6: 51,458,726 (GRCm39)	P64S	probably benign	Het
Chchd6	A	G	6: 89,544,567 (GRCm39)		probably null	Het
Cntn1	G	A	15: 92,212,534 (GRCm39)	E899K	probably benign	Het
Col6a4	A	T	9: 105,949,387 (GRCm39)	S749R	possibly damaging	Het
Cpne3	T	G	4: 19,553,779 (GRCm39)	N84T	probably benign	Het
Dcxr	A	C	11: 120,617,025 (GRCm39)		probably benign	Het
Dnhd1	G	A	7: 105,352,416 (GRCm39)	R2523Q	probably damaging	Het
Emsy	T	C	7: 98,242,818 (GRCm39)	Q1107R	possibly damaging	Het
Erbb2	G	T	11: 98,313,596 (GRCm39)	C221F	probably damaging	Het
Exoc3l	T	C	8: 106,019,795 (GRCm39)	N353D	probably benign	Het
Fchsd1	C	T	18: 38,092,926 (GRCm39)		probably benign	Het
G3bp2	T	A	5: 92,216,347 (GRCm39)	H63L	probably benign	Het
Galnt17	A	G	5: 130,929,428 (GRCm39)	Y460H	probably damaging	Het
Gm6003	T	A	7: 32,865,004 (GRCm39)		noncoding transcript	Het
Ighv5-12-4	A	G	12: 113,726,154 (GRCm39)	L23P	probably damaging	Het
Ins1	T	C	19: 52,253,177 (GRCm39)	L39P	probably damaging	Het
Itpr3	T	G	17: 27,306,566 (GRCm39)	V210G	probably damaging	Het
Klrb1	T	A	6: 128,683,488 (GRCm39)	T210S	probably benign	Het
Krtap24-1	A	T	16: 88,408,596 (GRCm39)	F177I	probably damaging	Het
Lrrc37	A	T	11: 103,506,079 (GRCm39)	I1963K	probably benign	Het
Mcat	A	G	15: 83,431,875 (GRCm39)		probably null	Het
Mknk2	A	T	10: 80,504,475 (GRCm39)	C229S	possibly damaging	Het
Mta2	C	A	19: 8,925,456 (GRCm39)	Q362K	probably benign	Het
Ndst4	T	C	3: 125,232,105 (GRCm39)	Y225H	probably benign	Het
Or4d11	T	C	19: 12,013,429 (GRCm39)	R226G	probably damaging	Het
Pcdha1	A	G	18: 37,065,415 (GRCm39)	D693G	probably benign	Het
Pik3r5	G	A	11: 68,368,294 (GRCm39)	D100N	possibly damaging	Het
Prkdc	T	C	16: 15,496,172 (GRCm39)	Y788H	probably damaging	Het
Ptprt	T	A	2: 162,120,143 (GRCm39)	D108V	probably damaging	Het
Rasgrp3	T	A	17: 75,823,354 (GRCm39)	M475K	probably benign	Het
Rbak	A	G	5: 143,159,064 (GRCm39)	L663P	probably damaging	Het
Rnf17	A	G	14: 56,719,590 (GRCm39)	N947D	probably damaging	Het
Ryr2	T	C	13: 11,702,795 (GRCm39)	S2898G	probably benign	Het
Serpina1e	A	C	12: 103,917,087 (GRCm39)	L194R	probably damaging	Het
Smg6	T	C	11: 74,944,724 (GRCm39)	S158P	probably damaging	Het
Smtnl2	A	T	11: 72,292,342 (GRCm39)	V269E	possibly damaging	Het
Snx14	G	T	9: 88,265,855 (GRCm39)	P760Q	probably damaging	Het
Sorl1	T	C	9: 41,948,508 (GRCm39)	E759G	possibly damaging	Het
Sspo	C	T	6: 48,473,588 (GRCm39)	T4906M	possibly damaging	Het
Syne2	T	A	12: 75,991,944 (GRCm39)	F1970I	possibly damaging	Het
Tekt3	C	A	11: 62,974,768 (GRCm39)	H362Q	probably benign	Het
Tmem121	T	C	12: 113,152,547 (GRCm39)	V255A	possibly damaging	Het
Tmem201	T	C	4: 149,802,534 (GRCm39)	T614A	probably benign	Het
Tnc	T	C	4: 63,935,916 (GRCm39)	D340G	probably damaging	Het
Ttc28	A	T	5: 111,373,794 (GRCm39)	T1046S	probably benign	Het
Ubxn2a	T	C	12: 4,952,238 (GRCm39)	D8G	probably benign	Het
Vwde	T	C	6: 13,186,937 (GRCm39)	N850S	probably benign	Het
Zfp280d	A	G	9: 72,231,417 (GRCm39)	H451R	probably damaging	Het
Zfp462	T	C	4: 55,009,818 (GRCm39)	C595R	probably damaging	Het
Zfp768	A	G	7: 126,943,583 (GRCm39)	S182P	probably benign	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
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
R9096:Pld3	UTSW	7	27,232,089 (GRCm39)	missense	probably benign	0.08
R9292:Pld3	UTSW	7	27,238,879 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- TGGAGAGTACAGAGCCACAC -3'
(R):5'- TCATACATTGGTAAGTGCCCC -3'

Sequencing Primer
(F):5'- TACAGAGCCACACGGGATAGAC -3'
(R):5'- ATTGGTAAGTGCCCCCAGTAC -3'

Posted On

2016-10-05