Mutagenetix > Incidental Mutation

Incidental Mutation 'R2513:Plod3'

253597

Institutional Source

Beutler Lab

Gene Symbol

Plod3

Ensembl Gene

ENSMUSG00000004846

Gene Name

procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3

Synonyms

LH3, lysyl hydroxylase 3

MMRRC Submission

040419-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2513 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

137015873-137025500 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 137017000 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Proline at position 50 (A50P)

Ref Sequence

ENSEMBL: ENSMUSP00000004968 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000004968] [ENSMUST00000034953] [ENSMUST00000085941] [ENSMUST00000111090] [ENSMUST00000111091] [ENSMUST00000156963] [ENSMUST00000137272]

AlphaFold

Q9R0E1

Predicted Effect

probably benign
Transcript: ENSMUST00000004968
AA Change: A50P

PolyPhen 2 Score 0.382 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: A50P

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
low complexity region	312	324	N/A	INTRINSIC
Blast:P4Hc	456	502	2e-8	BLAST
P4Hc	567	740	1.43e-23	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000034953

SMART Domains

Protein: ENSMUSP00000034953
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	14	26	N/A	INTRINSIC
low complexity region	58	73	N/A	INTRINSIC
Pfam:zf-HIT	112	141	6.3e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000085941

SMART Domains

Protein: ENSMUSP00000083103
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	15	27	N/A	INTRINSIC
low complexity region	59	74	N/A	INTRINSIC
Pfam:zf-HIT	113	142	3e-13	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000102285

Predicted Effect

probably benign
Transcript: ENSMUST00000111090

SMART Domains

Protein: ENSMUSP00000106719
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	14	26	N/A	INTRINSIC
low complexity region	58	73	N/A	INTRINSIC
Pfam:zf-HIT	112	141	2.2e-14	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000111091

SMART Domains

Protein: ENSMUSP00000106720
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	19	31	N/A	INTRINSIC
low complexity region	63	78	N/A	INTRINSIC
Pfam:zf-HIT	117	146	2.1e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000127100

SMART Domains

Protein: ENSMUSP00000123550
Gene: ENSMUSG00000004846

Domain	Start	End	E-Value	Type
Blast:P4Hc	2	35	2e-11	BLAST
P4Hc	38	200	3.04e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144784

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137419

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151642

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129896

Predicted Effect

probably benign
Transcript: ENSMUST00000156963

SMART Domains

Protein: ENSMUSP00000115929
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	14	26	N/A	INTRINSIC
low complexity region	58	73	N/A	INTRINSIC
Pfam:zf-HIT	112	141	6.7e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000137272

SMART Domains

Protein: ENSMUSP00000120331
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	19	31	N/A	INTRINSIC

Meta Mutation Damage Score

0.1039

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VIB have deficiencies in lysyl hydroxylase activity. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice display embryonic lethality, reduced embryonic growth, fragility, and fragmented basement membranes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	T	C	14: 32,383,809 (GRCm39)	T719A	possibly damaging	Het
Abcc1	A	G	16: 14,290,873 (GRCm39)		probably null	Het
Aftph	C	T	11: 20,658,676 (GRCm39)		probably null	Het
Als2	C	A	1: 59,254,276 (GRCm39)	K360N	probably benign	Het
Atg2a	T	A	19: 6,308,076 (GRCm39)		probably null	Het
Axl	T	C	7: 25,486,941 (GRCm39)	D22G	probably benign	Het
Baiap2	G	A	11: 119,890,052 (GRCm39)	A438T	probably benign	Het
Bean1	G	C	8: 104,908,643 (GRCm39)	A7P	probably benign	Het
Birc6	C	G	17: 74,954,724 (GRCm39)	P3431R	probably damaging	Het
Camk1d	A	G	2: 5,719,047 (GRCm39)	M1T	probably null	Het
Carmil3	T	C	14: 55,741,295 (GRCm39)	Y1027H	probably damaging	Het
Ccdc6	G	A	10: 70,023,658 (GRCm39)		probably benign	Het
Cemip	C	A	7: 83,591,233 (GRCm39)	V1280L	probably benign	Het
Cfap58	C	A	19: 47,950,981 (GRCm39)	N447K	probably benign	Het
Chd3	A	G	11: 69,251,471 (GRCm39)	L520P	probably damaging	Het
Col1a2	T	A	6: 4,531,223 (GRCm39)		probably null	Het
Cpne7	A	C	8: 123,844,406 (GRCm39)		probably null	Het
Ctla4	T	C	1: 60,951,723 (GRCm39)	V84A	probably damaging	Het
Dap3	A	G	3: 88,835,565 (GRCm39)	V263A	probably benign	Het
Dhx57	T	A	17: 80,549,378 (GRCm39)		probably null	Het
Dlg5	C	A	14: 24,214,593 (GRCm39)	K663N	probably damaging	Het
Dsg3	C	A	18: 20,656,719 (GRCm39)	F196L	possibly damaging	Het
Eif2ak4	C	A	2: 118,257,064 (GRCm39)	D402E	probably damaging	Het
Fance	T	C	17: 28,537,068 (GRCm39)	V24A	probably benign	Het
Fasn	A	T	11: 120,705,574 (GRCm39)	L1149Q	probably damaging	Het
Fcgbpl1	C	G	7: 27,831,060 (GRCm39)	S91C	probably damaging	Het
Flg	T	A	3: 93,187,093 (GRCm39)	S182T	possibly damaging	Het
Gm128	T	A	3: 95,147,293 (GRCm39)	S334C	possibly damaging	Het
Gm3727	A	C	14: 7,264,561 (GRCm38)	H31Q	probably damaging	Het
Gm4841	T	G	18: 60,403,977 (GRCm39)	T39P	probably damaging	Het
Golgb1	G	T	16: 36,735,513 (GRCm39)	V1587L	possibly damaging	Het
Golm1	G	A	13: 59,790,072 (GRCm39)	P243S	probably benign	Het
Gstcd	C	A	3: 132,788,081 (GRCm39)	A206S	possibly damaging	Het
Gstcd	C	A	3: 132,788,082 (GRCm39)	K205N	possibly damaging	Het
Gtf3c1	A	G	7: 125,280,345 (GRCm39)	V355A	probably benign	Het
Hhatl	T	C	9: 121,618,236 (GRCm39)	D173G	probably benign	Het
Kcnu1	T	A	8: 26,395,994 (GRCm39)	C660S	probably benign	Het
Kctd8	T	C	5: 69,267,988 (GRCm39)	D374G	probably benign	Het
Kif21a	T	C	15: 90,878,594 (GRCm39)	I229V	possibly damaging	Het
L3mbtl1	A	T	2: 162,809,505 (GRCm39)	I702F	probably benign	Het
Lce1d	T	C	3: 92,593,066 (GRCm39)		probably benign	Het
Lrig1	C	T	6: 94,594,347 (GRCm39)		probably null	Het
Lrp12	A	T	15: 39,739,507 (GRCm39)	D563E	probably damaging	Het
Lrp2	C	T	2: 69,336,718 (GRCm39)		probably null	Het
Map3k5	G	A	10: 19,970,201 (GRCm39)	V703I	possibly damaging	Het
Mecr	A	G	4: 131,581,076 (GRCm39)	R110G	probably benign	Het
Mtrr	T	A	13: 68,715,092 (GRCm39)	K445*	probably null	Het
Nanos1	T	A	19: 60,744,990 (GRCm39)	L96Q	probably benign	Het
Or13a24	T	G	7: 140,154,069 (GRCm39)	M1R	probably null	Het
Or51t4	T	A	7: 102,598,700 (GRCm39)	F333I	probably benign	Het
Or6c214	T	A	10: 129,591,021 (GRCm39)	L99F	probably damaging	Het
Otog	T	C	7: 45,955,014 (GRCm39)		probably null	Het
Pcdhb3	G	T	18: 37,434,294 (GRCm39)	V87F	probably benign	Het
Pcdhb3	T	A	18: 37,434,292 (GRCm39)	L86*	probably null	Het
Pcdhb3	A	T	18: 37,434,293 (GRCm39)	L86F	probably damaging	Het
Pdgfd	A	G	9: 6,359,894 (GRCm39)	K322E	probably damaging	Het
Picalm	T	C	7: 89,846,217 (GRCm39)	S648P	probably damaging	Het
Pigr	T	C	1: 130,774,357 (GRCm39)	S446P	possibly damaging	Het
Pik3cb	A	C	9: 98,943,895 (GRCm39)	L636W	probably damaging	Het
Pla2g2f	A	T	4: 138,481,473 (GRCm39)	L92Q	probably damaging	Het
Prkar2b	C	T	12: 32,025,928 (GRCm39)	V191I	possibly damaging	Het
Prune1	C	A	3: 95,165,430 (GRCm39)	A281S	probably benign	Het
Ptges3l	A	T	11: 101,314,868 (GRCm39)	C42S	possibly damaging	Het
Reg3b	A	T	6: 78,348,802 (GRCm39)	I33L	probably benign	Het
Rel	A	G	11: 23,695,823 (GRCm39)	I188T	probably damaging	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Ripor1	G	T	8: 106,344,254 (GRCm39)	V463L	probably benign	Het
Rrm1	T	A	7: 102,109,896 (GRCm39)	D510E	probably damaging	Het
Setd7	A	G	3: 51,440,436 (GRCm39)	S202P	probably damaging	Het
Shank3	T	A	15: 89,432,889 (GRCm39)	D1211E	probably benign	Het
Slc30a1	A	T	1: 191,639,674 (GRCm39)	T186S	possibly damaging	Het
Slc4a4	G	A	5: 89,304,257 (GRCm39)	V523I	probably benign	Het
Slc9a2	T	A	1: 40,781,768 (GRCm39)		probably null	Het
Smg6	A	G	11: 74,820,502 (GRCm39)	T258A	probably damaging	Het
Sptlc1	C	T	13: 53,491,676 (GRCm39)	D408N	possibly damaging	Het
Tasor2	G	T	13: 3,632,150 (GRCm39)	L784I	possibly damaging	Het
Tbl3	T	C	17: 24,923,524 (GRCm39)		probably null	Het
Tdo2	T	C	3: 81,876,812 (GRCm39)	D139G	possibly damaging	Het
Ticam1	T	A	17: 56,578,612 (GRCm39)	H161L	possibly damaging	Het
Tnfaip3	T	A	10: 18,881,407 (GRCm39)	D293V	probably benign	Het
Trim72	G	A	7: 127,603,878 (GRCm39)	V75M	possibly damaging	Het
Trip11	T	A	12: 101,803,986 (GRCm39)	N1632I	possibly damaging	Het
Tspan18	A	T	2: 93,050,440 (GRCm39)	M61K	possibly damaging	Het
Tuba8	A	T	6: 121,202,932 (GRCm39)	E415V	probably damaging	Het
Ung	A	G	5: 114,275,253 (GRCm39)	H214R	probably benign	Het
Uqcrc1	T	C	9: 108,765,836 (GRCm39)	L17P	probably damaging	Het
Usp24	A	G	4: 106,236,602 (GRCm39)		probably null	Het
Vps39	A	C	2: 120,169,268 (GRCm39)	Y245D	probably damaging	Het
Whrn	T	A	4: 63,353,649 (GRCm39)	T373S	probably benign	Het
Zc2hc1a	C	T	3: 7,581,596 (GRCm39)		probably null	Het

Other mutations in Plod3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00507:Plod3	APN	5	137,025,030 (GRCm39)	missense	possibly damaging	0.78
IGL01090:Plod3	APN	5	137,019,090 (GRCm39)	missense	probably benign	0.37
IGL01443:Plod3	APN	5	137,019,075 (GRCm39)	missense	probably benign	0.17
IGL01583:Plod3	APN	5	137,025,002 (GRCm39)	missense	probably benign	0.02
R0544:Plod3	UTSW	5	137,020,465 (GRCm39)	missense	probably benign	0.09
R0747:Plod3	UTSW	5	137,017,049 (GRCm39)	missense	probably benign	0.34
R0764:Plod3	UTSW	5	137,018,437 (GRCm39)	unclassified	probably benign
R1520:Plod3	UTSW	5	137,020,165 (GRCm39)	missense	probably damaging	0.99
R1631:Plod3	UTSW	5	137,017,847 (GRCm39)	missense	probably damaging	1.00
R1751:Plod3	UTSW	5	137,019,030 (GRCm39)	missense	possibly damaging	0.89
R1767:Plod3	UTSW	5	137,019,030 (GRCm39)	missense	possibly damaging	0.89
R1984:Plod3	UTSW	5	137,019,707 (GRCm39)	splice site	probably null
R1985:Plod3	UTSW	5	137,019,707 (GRCm39)	splice site	probably null
R2137:Plod3	UTSW	5	137,017,571 (GRCm39)	missense	probably damaging	1.00
R2148:Plod3	UTSW	5	137,016,627 (GRCm39)	nonsense	probably null
R2179:Plod3	UTSW	5	137,019,862 (GRCm39)	missense	possibly damaging	0.77
R2318:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2319:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2512:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2696:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2891:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2893:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R3030:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R3439:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R3957:Plod3	UTSW	5	137,023,046 (GRCm39)	missense	probably damaging	1.00
R4080:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4081:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4342:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4344:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4345:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4546:Plod3	UTSW	5	137,017,801 (GRCm39)	missense	possibly damaging	0.94
R4799:Plod3	UTSW	5	137,019,654 (GRCm39)	missense	probably benign	0.00
R4843:Plod3	UTSW	5	137,019,854 (GRCm39)	nonsense	probably null
R4956:Plod3	UTSW	5	137,018,772 (GRCm39)	missense	probably damaging	1.00
R5159:Plod3	UTSW	5	137,023,932 (GRCm39)	intron	probably benign
R5162:Plod3	UTSW	5	137,020,161 (GRCm39)	missense	probably damaging	1.00
R5328:Plod3	UTSW	5	137,018,537 (GRCm39)	missense	probably damaging	1.00
R5427:Plod3	UTSW	5	137,020,642 (GRCm39)	missense	probably damaging	1.00
R6627:Plod3	UTSW	5	137,017,310 (GRCm39)	missense	probably damaging	0.99
R7003:Plod3	UTSW	5	137,018,498 (GRCm39)	missense	probably damaging	1.00
R7132:Plod3	UTSW	5	137,023,971 (GRCm39)	missense
R7376:Plod3	UTSW	5	137,019,335 (GRCm39)	missense	probably benign	0.00
R7404:Plod3	UTSW	5	137,023,901 (GRCm39)	missense	probably benign
R7827:Plod3	UTSW	5	137,018,835 (GRCm39)	missense	probably benign
R8062:Plod3	UTSW	5	137,019,123 (GRCm39)	missense	possibly damaging	0.87
R8506:Plod3	UTSW	5	137,017,830 (GRCm39)	missense	probably damaging	1.00
R8772:Plod3	UTSW	5	137,017,773 (GRCm39)	missense	probably damaging	0.99
R9108:Plod3	UTSW	5	137,018,017 (GRCm39)	missense	probably damaging	0.99
R9439:Plod3	UTSW	5	137,023,036 (GRCm39)	missense	probably benign	0.03
R9788:Plod3	UTSW	5	137,019,911 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CTCTTCTGGAGATCAAATGTGC -3'
(R):5'- ACTGTTCGAGCCACATCACC -3'

Sequencing Primer
(F):5'- CTTCTGGAGATCAAATGTGCTGAAAG -3'
(R):5'- CCCAGGGTCTGCAGGAAAGATC -3'

Posted On

2014-12-04