Mutagenetix > Incidental Mutation

Incidental Mutation 'R0764:Plod3'

72547

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

038944-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0764 (G1)

Quality Score

193

Status

Validated

Chromosome

Chromosomal Location

136987019-136996648 bp(+) (GRCm38)

Type of Mutation

unclassified

DNA Base Change (assembly)

C to T at 136989583 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000115929 (fasta)

Gene Model

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

AlphaFold

Q9R0E1

Predicted Effect

probably benign
Transcript: ENSMUST00000004968

SMART Domains

Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846

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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.1%

Validation Efficiency

98% (48/49)

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8a	A	T	11: 110,059,946	Y898N	probably damaging	Het
Acp4	T	C	7: 44,252,314		probably benign	Het
Adipor2	T	C	6: 119,357,254	I332V	probably benign	Het
Ago3	T	A	4: 126,355,092	K555N	possibly damaging	Het
Angpt4	A	G	2: 151,911,284		probably benign	Het
Ano5	G	T	7: 51,537,842		probably benign	Het
Ap3b1	C	T	13: 94,479,879		probably benign	Het
BC025446	T	A	15: 75,220,723	F97Y	probably benign	Het
Cbl	A	T	9: 44,164,152	C399S	probably damaging	Het
Cdkl2	C	A	5: 92,020,277	V353L	probably benign	Het
Celsr3	A	G	9: 108,827,818	Y500C	probably damaging	Het
Cep162	A	G	9: 87,201,745	S1242P	probably damaging	Het
Crhr1	C	T	11: 104,159,326	R66W	probably damaging	Het
Ddx49	T	C	8: 70,297,257	E170G	probably benign	Het
Fam193a	T	C	5: 34,443,341	F305L	probably damaging	Het
Fam76a	C	T	4: 132,910,699	G198R	probably damaging	Het
Gm43302	T	A	5: 105,280,489	I130F	probably benign	Het
Hectd4	T	A	5: 121,286,769	I745N	possibly damaging	Het
Ina	T	A	19: 47,023,648	*502K	probably null	Het
Kdm1b	A	T	13: 47,068,603	D506V	possibly damaging	Het
Lrrk2	A	G	15: 91,775,046		probably null	Het
Naip5	A	T	13: 100,217,105	D1215E	probably benign	Het
Neb	A	G	2: 52,216,867		probably benign	Het
Nectin2	T	A	7: 19,749,171		probably null	Het
Nup155	A	T	15: 8,157,760	H1391L	probably damaging	Het
Olfr1243	A	G	2: 89,527,996	V138A	probably benign	Het
Olfr170	G	T	16: 19,606,432	P79T	probably damaging	Het
Osbp	A	G	19: 11,984,156		probably benign	Het
Otog	A	G	7: 46,300,494	D2460G	probably benign	Het
Pcgf1	T	C	6: 83,079,169	C2R	probably damaging	Het
Per2	C	T	1: 91,429,420	V674M	probably damaging	Het
Pias3	C	T	3: 96,701,295	P218S	probably damaging	Het
Purb	C	T	11: 6,475,661	V76M	probably damaging	Het
Ranbp1	C	A	16: 18,240,158	E181*	probably null	Het
Rit2	T	C	18: 31,153,701		probably benign	Het
Rnf103	C	A	6: 71,509,582	T399K	probably damaging	Het
Slc22a13	T	C	9: 119,208,680		probably null	Het
Slc35f4	T	A	14: 49,306,339		probably benign	Het
Sucla2	C	T	14: 73,560,634		probably benign	Het
Tnfrsf17	C	T	16: 11,315,199	T47M	possibly damaging	Het
Tram1	A	G	1: 13,579,709	I97T	probably damaging	Het
Ttc38	T	C	15: 85,846,403		probably benign	Het
Zfp113	T	A	5: 138,145,244	Q248L	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
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
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
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'- TCAATGGAGCCTTAGGTGAGGACG -3'
(R):5'- GGCACCCTTTTCTGCTGGAAATGG -3'

Sequencing Primer
(F):5'- gagcacctgcctagaatcc -3'
(R):5'- TTTCTGCTGGAAATGGAGAAAACC -3'

Posted On

2013-09-30