Mutagenetix > Incidental Mutation

Incidental Mutation 'R9049:Pld3'

688239

Institutional Source

Beutler Lab

Gene Symbol

Pld3

Ensembl Gene

ENSMUSG00000003363

Gene Name

phospholipase D family member 3

Synonyms

Sam-9

MMRRC Submission

068875-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9049 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

27231425-27252643 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 27235293 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 312 (V312M)

Ref Sequence

ENSEMBL: ENSMUSP00000113820 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000037134] [ENSMUST00000108353] [ENSMUST00000117095] [ENSMUST00000117611] [ENSMUST00000131106]

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

possibly damaging
Transcript: ENSMUST00000117095
AA Change: V312M

PolyPhen 2 Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000113820
Gene: ENSMUSG00000003363
AA Change: V312M

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

possibly damaging
Transcript: ENSMUST00000117611
AA Change: V312M

PolyPhen 2 Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000112942
Gene: ENSMUSG00000003363
AA Change: V312M

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

probably benign
Transcript: ENSMUST00000131106

Meta Mutation Damage Score

0.1455

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.8%

Validation Efficiency

100% (64/64)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110009E18Rik	A	G	1: 120,115,900 (GRCm39)	I118V	probably null	Het
Abcc9	A	G	6: 142,628,658 (GRCm39)	L362P	probably damaging	Het
Adam7	C	A	14: 68,762,674 (GRCm39)	V184F	probably benign	Het
Adgre4	T	C	17: 56,092,094 (GRCm39)	I118T	probably benign	Het
Akap9	T	C	5: 4,114,597 (GRCm39)	L3292P		Het
Akr1b10	A	G	6: 34,373,561 (GRCm39)	E308G	possibly damaging	Het
Aopep	A	G	13: 63,208,852 (GRCm39)	Y323C	probably benign	Het
Ash1l	T	C	3: 88,914,671 (GRCm39)	V1767A	probably benign	Het
Bpifb3	C	A	2: 153,767,810 (GRCm39)	N294K	probably benign	Het
Bpifb5	A	G	2: 154,070,096 (GRCm39)	N182S	probably benign	Het
C9orf72	A	G	4: 35,192,964 (GRCm39)	I455T	unknown	Het
Camkmt	A	G	17: 85,709,912 (GRCm39)	I205M	possibly damaging	Het
Ccdc88b	C	T	19: 6,826,442 (GRCm39)	R1091Q	probably benign	Het
Cfap58	A	T	19: 48,015,157 (GRCm39)		probably null	Het
Clca3a1	T	A	3: 144,733,143 (GRCm39)	I122L	probably benign	Het
Col6a3	T	A	1: 90,707,066 (GRCm39)	S2623C	unknown	Het
Cpne5	A	G	17: 29,379,332 (GRCm39)	S484P	probably damaging	Het
Cyp4f39	T	A	17: 32,705,965 (GRCm39)	L352Q	probably damaging	Het
Dcun1d1	T	C	3: 35,951,998 (GRCm39)	N183D	probably benign	Het
Dgkg	A	G	16: 22,419,338 (GRCm39)	V54A	probably benign	Het
Dnah12	T	A	14: 26,443,275 (GRCm39)	D561E	probably benign	Het
Dnah6	A	C	6: 73,119,275 (GRCm39)	L1536R	probably damaging	Het
Gm21834	G	A	17: 58,048,826 (GRCm39)	T130I	possibly damaging	Het
Hectd4	T	A	5: 121,451,955 (GRCm39)	V434E	possibly damaging	Het
Htr3a	C	A	9: 48,811,087 (GRCm39)	V459L	probably damaging	Het
Lonp2	T	C	8: 87,435,735 (GRCm39)	V657A	probably benign	Het
Mdfi	C	A	17: 48,135,479 (GRCm39)	V84L	probably damaging	Het
Mdm1	C	T	10: 117,982,605 (GRCm39)	T80M	probably benign	Het
Muc5ac	A	C	7: 141,362,712 (GRCm39)	I2008L	unknown	Het
Nomo1	A	G	7: 45,715,597 (GRCm39)	D681G	probably benign	Het
Or10g9	G	T	9: 39,911,919 (GRCm39)	N201K	possibly damaging	Het
Or14j6	G	A	17: 38,214,764 (GRCm39)	W109*	probably null	Het
Or1af1	C	G	2: 37,109,959 (GRCm39)	H153D	probably damaging	Het
Or1p1c	A	G	11: 74,161,115 (GRCm39)	K300R	possibly damaging	Het
Or5h25	T	G	16: 58,930,763 (GRCm39)	D70A	probably damaging	Het
Or5m5	A	G	2: 85,814,235 (GRCm39)	E17G	possibly damaging	Het
Or7e169	T	C	9: 19,757,045 (GRCm39)	Y290C	probably damaging	Het
Pip5k1c	C	A	10: 81,152,710 (GRCm39)		probably benign	Het
Pipox	A	G	11: 77,772,380 (GRCm39)	I330T	probably damaging	Het
Pira13	T	A	7: 3,819,890 (GRCm39)	T676S	unknown	Het
Pnisr	T	A	4: 21,854,391 (GRCm39)	W12R	unknown	Het
Polr3e	A	G	7: 120,538,462 (GRCm39)	K410R	probably benign	Het
Ppif	G	T	14: 25,694,836 (GRCm39)	V61L	possibly damaging	Het
Pramel5	T	C	4: 144,000,486 (GRCm39)	N30S	probably benign	Het
Prex2	T	G	1: 11,256,130 (GRCm39)	L1167R	probably damaging	Het
Prkacb	A	T	3: 146,461,518 (GRCm39)		probably benign	Het
Prl3a1	T	A	13: 27,460,167 (GRCm39)	L217H	probably damaging	Het
Prop1	G	C	11: 50,842,948 (GRCm39)	Q80E	probably damaging	Het
Psma1	T	C	7: 113,865,764 (GRCm39)	I214V	probably benign	Het
Ptgfr	T	A	3: 151,541,404 (GRCm39)	I35F	probably benign	Het
Rcvrn	A	T	11: 67,586,568 (GRCm39)	Y109F	probably benign	Het
Repin1	A	G	6: 48,574,646 (GRCm39)	D525G	possibly damaging	Het
Slc12a2	A	T	18: 58,054,863 (GRCm39)	R835*	probably null	Het
Sqle	T	C	15: 59,189,711 (GRCm39)	F118L	probably benign	Het
Stard9	A	T	2: 120,510,418 (GRCm39)	Y333F	probably benign	Het
Tbc1d16	G	A	11: 119,100,090 (GRCm39)	R95C	probably damaging	Het
Tln1	C	A	4: 43,549,786 (GRCm39)	E542*	probably null	Het
Tmem161b	G	T	13: 84,442,754 (GRCm39)	A407S	probably benign	Het
Tnc	G	T	4: 63,918,247 (GRCm39)	D1221E	possibly damaging	Het
Tnks	T	C	8: 35,308,932 (GRCm39)	K1109R	probably damaging	Het
Tpp2	T	C	1: 43,992,502 (GRCm39)	V194A	possibly damaging	Het
Ust	G	A	10: 8,183,218 (GRCm39)	Q162*	probably null	Het
Utp15	T	C	13: 98,395,778 (GRCm39)	Y68C	probably damaging	Het
Vcan	A	T	13: 89,826,224 (GRCm39)	H3193Q	probably damaging	Het
Vmn2r55	T	C	7: 12,418,908 (GRCm39)	Y4C	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
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'- TATCTGCTGTCCTGCCTGGG -3'
(R):5'- CTGTACATCATACATAGGCATACATC -3'

Sequencing Primer
(F):5'- GGACCCCCTGCTTGCTGTC -3'
(R):5'- AGTAACAGAGTGCCCCTATTGCTG -3'

Posted On

2021-11-19