Mutagenetix > Incidental Mutation

Incidental Mutation 'R5162:Plod3'

397045

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

042744-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5162 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

136987019-136996648 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 136991307 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 459 (W459R)

Ref Sequence

ENSEMBL: ENSMUSP00000004968 (fasta)

Gene Model

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

AlphaFold

Q9R0E1

Predicted Effect

probably damaging
Transcript: ENSMUST00000004968
AA Change: W459R

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

SMART Domains

Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: W459R

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

0.9525

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.2%
20x: 94.8%

Validation Efficiency

98% (61/62)

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010315B03Rik	T	A	9: 124,293,671	T229S	probably benign	Het
Adrb3	T	C	8: 27,227,320	E367G	probably benign	Het
Ak9	T	A	10: 41,357,657	N630K	probably damaging	Het
Atp8b1	T	C	18: 64,561,662	I516M	possibly damaging	Het
Bcor	C	T	X: 12,040,486	R1551Q	probably damaging	Het
Cry1	T	A	10: 85,133,286	H558L	probably benign	Het
Cyp3a57	T	A	5: 145,369,083	W126R	probably damaging	Het
Dhx36	A	T	3: 62,493,780	V355E	probably damaging	Het
Diexf	G	T	1: 193,113,781	T192K	probably damaging	Het
Dpp6	A	G	5: 27,399,015		probably benign	Het
Ehmt1	G	T	2: 24,877,497	P135T	probably damaging	Het
Enpp2	T	C	15: 54,847,296	D694G	probably benign	Het
Esrp2	T	C	8: 106,133,298	E336G	probably damaging	Het
Faah	A	T	4: 116,000,741		probably benign	Het
Fat1	G	A	8: 45,025,809	G2608R	probably benign	Het
Fbxo8	A	T	8: 56,569,319	Y122F	probably damaging	Het
Fgd5	A	G	6: 92,074,234	D1497G	probably damaging	Het
Fn3krp	T	C	11: 121,429,584	F252L	probably damaging	Het
Fnip2	T	C	3: 79,481,777	Y549C	probably damaging	Het
Gcm2	T	C	13: 41,103,655	N206S	probably benign	Het
Gm4758	A	T	16: 36,312,556	H65L	probably damaging	Het
Grn	C	A	11: 102,430,554		probably benign	Het
H2-T10	T	A	17: 36,118,951		probably null	Het
Henmt1	T	C	3: 108,940,050		probably null	Het
Man1b1	T	A	2: 25,343,353	L246Q	probably damaging	Het
Mdh2	T	C	5: 135,783,475		probably null	Het
Mocos	T	C	18: 24,654,052	F43L	probably damaging	Het
Mpp6	T	A	6: 50,178,515	W259R	probably damaging	Het
Msh2	C	A	17: 87,723,413	A906E	probably benign	Het
Naip5	T	A	13: 100,223,406	I441F	possibly damaging	Het
Naip6	C	T	13: 100,300,600	A472T	probably benign	Het
Nars2	T	C	7: 97,059,820		probably benign	Het
Ncoa2	A	T	1: 13,175,172	M434K	possibly damaging	Het
Nlrp4g	T	A	9: 124,350,394		noncoding transcript	Het
Olfr459	G	T	6: 41,771,772	H176N	possibly damaging	Het
Olfr761	T	A	17: 37,952,364	Q220L	probably benign	Het
Pars2	A	G	4: 106,654,538	T506A	probably benign	Het
Pkp2	T	C	16: 16,260,336	S481P	probably damaging	Het
Pramef12	A	T	4: 144,394,912	L181M	probably damaging	Het
Prdm10	A	T	9: 31,340,418	I361F	possibly damaging	Het
Ptpro	T	A	6: 137,443,594	V1007D	probably damaging	Het
Raver2	T	C	4: 101,102,724	C134R	probably damaging	Het
Rnf130	G	C	11: 50,052,895	A123P	probably damaging	Het
Slc29a4	G	A	5: 142,721,452	A517T	possibly damaging	Het
Slc38a6	T	A	12: 73,329,985	S138T	possibly damaging	Het
Spred1	T	C	2: 117,177,621	V336A	possibly damaging	Het
Sptlc3	T	A	2: 139,631,343	M504K	probably benign	Het
Syt11	T	C	3: 88,747,842	D78G	probably damaging	Het
Trim23	C	T	13: 104,181,174	T61I	probably damaging	Het
Tsg101	T	C	7: 46,892,426	T260A	probably damaging	Het
Tyw5	T	C	1: 57,401,459	Y48C	probably damaging	Het
Vmn1r17	A	G	6: 57,360,843	V130A	probably benign	Het
Vmn2r89	C	A	14: 51,456,163	H323Q	possibly damaging	Het
Vps18	A	G	2: 119,292,942	S117G	probably benign	Het
Zfp93	C	G	7: 24,276,332	Q581E	probably damaging	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
R2513: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
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
R8062:Plod3	UTSW	5	136990269	missense	possibly damaging	0.87
R8506:Plod3	UTSW	5	136988976	missense	probably damaging	1.00
R8772:Plod3	UTSW	5	136988919	missense	probably damaging	0.99
R9108:Plod3	UTSW	5	136989163	missense	probably damaging	0.99
R9439:Plod3	UTSW	5	136994182	missense	probably benign	0.03
R9788:Plod3	UTSW	5	136991057	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AAGACTACGTGGAACTGGTGC -3'
(R):5'- AACTCGTGCTGGTTGCTGAG -3'

Sequencing Primer
(F):5'- AAGCGAGTGTGAGTCCCAC -3'
(R):5'- ACATCAGGAGGCTGTGGGC -3'

Posted On

2016-06-21