Mutagenetix > Incidental Mutations

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

lysyl hydroxylase 3, LH3

MMRRC Submission

040419-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R2513 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

136987019-136996648 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 136988146 bp

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] [ENSMUST00000137272] [ENSMUST00000156963]

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: ENSMUST00000129896

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137419

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144784

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151642

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

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: 32,661,852	T719A	possibly damaging	Het
9530053A07Rik	C	G	7: 28,131,635	S91C	probably damaging	Het
Abcc1	A	G	16: 14,473,009		probably null	Het
Aftph	C	T	11: 20,708,676		probably null	Het
Als2	C	A	1: 59,215,117	K360N	probably benign	Het
Atg2a	T	A	19: 6,258,046		probably null	Het
Axl	T	C	7: 25,787,516	D22G	probably benign	Het
Baiap2	G	A	11: 119,999,226	A438T	probably benign	Het
Bean1	G	C	8: 104,182,011	A7P	probably benign	Het
Birc6	C	G	17: 74,647,729	P3431R	probably damaging	Het
Camk1d	A	G	2: 5,714,236	M1T	probably null	Het
Carmil3	T	C	14: 55,503,838	Y1027H	probably damaging	Het
Ccdc6	G	A	10: 70,187,828		probably benign	Het
Cemip	C	A	7: 83,942,025	V1280L	probably benign	Het
Cfap58	C	A	19: 47,962,542	N447K	probably benign	Het
Chd3	A	G	11: 69,360,645	L520P	probably damaging	Het
Col1a2	T	A	6: 4,531,223		probably null	Het
Cpne7	A	C	8: 123,117,667		probably null	Het
Ctla4	T	C	1: 60,912,564	V84A	probably damaging	Het
Dap3	A	G	3: 88,928,258	V263A	probably benign	Het
Dhx57	T	A	17: 80,241,949		probably null	Het
Dlg5	C	A	14: 24,164,525	K663N	probably damaging	Het
Dsg3	C	A	18: 20,523,662	F196L	possibly damaging	Het
Eif2ak4	C	A	2: 118,426,583	D402E	probably damaging	Het
Fam208b	G	T	13: 3,582,150	L784I	possibly damaging	Het
Fance	T	C	17: 28,318,094	V24A	probably benign	Het
Fasn	A	T	11: 120,814,748	L1149Q	probably damaging	Het
Flg	T	A	3: 93,279,786	S182T	possibly damaging	Het
Gm128	T	A	3: 95,239,982	S334C	possibly damaging	Het
Gm3727	A	C	14: 7,264,561	H31Q	probably damaging	Het
Gm4841	T	G	18: 60,270,905	T39P	probably damaging	Het
Golgb1	G	T	16: 36,915,151	V1587L	possibly damaging	Het
Golm1	G	A	13: 59,642,258	P243S	probably benign	Het
Gstcd	C	A	3: 133,082,320	A206S	possibly damaging	Het
Gstcd	C	A	3: 133,082,321	K205N	possibly damaging	Het
Gtf3c1	A	G	7: 125,681,173	V355A	probably benign	Het
Hhatl	T	C	9: 121,789,170	D173G	probably benign	Het
Kcnu1	T	A	8: 25,905,966	C660S	probably benign	Het
Kctd8	T	C	5: 69,110,645	D374G	probably benign	Het
Kif21a	T	C	15: 90,994,391	I229V	possibly damaging	Het
L3mbtl1	A	T	2: 162,967,585	I702F	probably benign	Het
Lce1d	T	C	3: 92,685,759		probably benign	Het
Lrig1	C	T	6: 94,617,366		probably null	Het
Lrp12	A	T	15: 39,876,111	D563E	probably damaging	Het
Lrp2	C	T	2: 69,506,374		probably null	Het
Map3k5	G	A	10: 20,094,455	V703I	possibly damaging	Het
Mecr	A	G	4: 131,853,765	R110G	probably benign	Het
Mtrr	T	A	13: 68,566,973	K445*	probably null	Het
Nanos1	T	A	19: 60,756,552	L96Q	probably benign	Het
Olfr538	T	G	7: 140,574,156	M1R	probably null	Het
Olfr574	T	A	7: 102,949,493	F333I	probably benign	Het
Olfr807	T	A	10: 129,755,152	L99F	probably damaging	Het
Otog	T	C	7: 46,305,590		probably null	Het
Pcdhb3	T	A	18: 37,301,239	L86*	probably null	Het
Pcdhb3	A	T	18: 37,301,240	L86F	probably damaging	Het
Pcdhb3	G	T	18: 37,301,241	V87F	probably benign	Het
Pdgfd	A	G	9: 6,359,894	K322E	probably damaging	Het
Picalm	T	C	7: 90,197,009	S648P	probably damaging	Het
Pigr	T	C	1: 130,846,620	S446P	possibly damaging	Het
Pik3cb	A	C	9: 99,061,842	L636W	probably damaging	Het
Pla2g2f	A	T	4: 138,754,162	L92Q	probably damaging	Het
Prkar2b	C	T	12: 31,975,929	V191I	possibly damaging	Het
Prune1	C	A	3: 95,258,119	A281S	probably benign	Het
Ptges3l	A	T	11: 101,424,042	C42S	possibly damaging	Het
Reg3b	A	T	6: 78,371,819	I33L	probably benign	Het
Rel	A	G	11: 23,745,823	I188T	probably damaging	Het
Rif1	GCCACCA	GCCA	2: 52,110,324		probably benign	Het
Ripor1	G	T	8: 105,617,622	V463L	probably benign	Het
Rrm1	T	A	7: 102,460,689	D510E	probably damaging	Het
Setd7	A	G	3: 51,533,015	S202P	probably damaging	Het
Shank3	T	A	15: 89,548,686	D1211E	probably benign	Het
Slc30a1	A	T	1: 191,907,562	T186S	possibly damaging	Het
Slc4a4	G	A	5: 89,156,398	V523I	probably benign	Het
Slc9a2	T	A	1: 40,742,608		probably null	Het
Smg6	A	G	11: 74,929,676	T258A	probably damaging	Het
Sptlc1	C	T	13: 53,337,640	D408N	possibly damaging	Het
Tbl3	T	C	17: 24,704,550		probably null	Het
Tdo2	T	C	3: 81,969,505	D139G	possibly damaging	Het
Ticam1	T	A	17: 56,271,612	H161L	possibly damaging	Het
Tnfaip3	T	A	10: 19,005,659	D293V	probably benign	Het
Trim72	G	A	7: 128,004,706	V75M	possibly damaging	Het
Trip11	T	A	12: 101,837,727	N1632I	possibly damaging	Het
Tspan18	A	T	2: 93,220,095	M61K	possibly damaging	Het
Tuba8	A	T	6: 121,225,973	E415V	probably damaging	Het
Ung	A	G	5: 114,137,192	H214R	probably benign	Het
Uqcrc1	T	C	9: 108,936,768	L17P	probably damaging	Het
Usp24	A	G	4: 106,379,405		probably null	Het
Vps39	A	C	2: 120,338,787	Y245D	probably damaging	Het
Whrn	T	A	4: 63,435,412	T373S	probably benign	Het
Zc2hc1a	C	T	3: 7,516,536		probably null	Het

Other mutations in Plod3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00507:Plod3	APN	5	136996176	missense	possibly damaging	0.78
IGL01090:Plod3	APN	5	136990236	missense	probably benign	0.37
IGL01443:Plod3	APN	5	136990221	missense	probably benign	0.17
IGL01583:Plod3	APN	5	136996148	missense	probably benign	0.02
R0544:Plod3	UTSW	5	136991611	missense	probably benign	0.09
R0747:Plod3	UTSW	5	136988195	missense	probably benign	0.34
R0764:Plod3	UTSW	5	136989583	unclassified	probably benign
R1520:Plod3	UTSW	5	136991311	missense	probably damaging	0.99
R1631:Plod3	UTSW	5	136988993	missense	probably damaging	1.00
R1751:Plod3	UTSW	5	136990176	missense	possibly damaging	0.89
R1767:Plod3	UTSW	5	136990176	missense	possibly damaging	0.89
R1984:Plod3	UTSW	5	136990853	splice site	probably null
R1985:Plod3	UTSW	5	136990853	splice site	probably null
R2137:Plod3	UTSW	5	136988717	missense	probably damaging	1.00
R2148:Plod3	UTSW	5	136987773	nonsense	probably null
R2179:Plod3	UTSW	5	136991008	missense	possibly damaging	0.77
R2318:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R2319:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R2512:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R2696:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R2891:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R2893:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R3030:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R3439:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R3957:Plod3	UTSW	5	136994192	missense	probably damaging	1.00
R4080:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R4081:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R4342:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R4344:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R4345:Plod3	UTSW	5	136988146	missense	probably benign	0.38
R4546:Plod3	UTSW	5	136988947	missense	possibly damaging	0.94
R4799:Plod3	UTSW	5	136990800	missense	probably benign	0.00
R4843:Plod3	UTSW	5	136991000	nonsense	probably null
R4956:Plod3	UTSW	5	136989918	missense	probably damaging	1.00
R5159:Plod3	UTSW	5	136995078	intron	probably benign
R5162:Plod3	UTSW	5	136991307	missense	probably damaging	1.00
R5328:Plod3	UTSW	5	136989683	missense	probably damaging	1.00
R5427:Plod3	UTSW	5	136991788	missense	probably damaging	1.00
R6627:Plod3	UTSW	5	136988456	missense	probably damaging	0.99
R7003:Plod3	UTSW	5	136989644	missense	probably damaging	1.00
R7132:Plod3	UTSW	5	136995117	missense
R7376:Plod3	UTSW	5	136990481	missense	probably benign	0.00
R7404:Plod3	UTSW	5	136995047	missense	probably benign
R7827:Plod3	UTSW	5	136989981	missense	probably benign

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