Mutagenetix > Incidental Mutations

Incidental Mutation 'R4342:Plod3'

324166

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

041100-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R4342 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

136987019-136996648 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 136988146 bp (GRCm38)

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]

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: 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: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.4%

Validation Efficiency

99% (68/69)

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aars2	T	C	17: 45,516,495	C488R	probably benign	Het
Adamts19	A	T	18: 58,942,500	H489L	probably damaging	Het
Ahnak	T	C	19: 9,012,083	V3577A	possibly damaging	Het
Arhgap44	G	A	11: 65,012,061	R401*	probably null	Het
Cbx3-ps2	T	C	13: 65,559,688		noncoding transcript	Het
Ccdc174	T	A	6: 91,885,356	L86*	probably null	Het
Cd38	A	C	5: 43,869,089	I72L	probably benign	Het
Cers4	T	C	8: 4,521,223	L264P	probably damaging	Het
Cldn23	A	G	8: 35,825,498	S279P	probably benign	Het
Cth	T	A	3: 157,924,976	T19S	probably damaging	Het
Dnajc22	T	A	15: 99,104,464	L330*	probably null	Het
Epas1	G	A	17: 86,823,800	C336Y	probably damaging	Het
Evi5l	A	C	8: 4,183,492		probably benign	Het
Fam71b	A	G	11: 46,407,216	D449G	possibly damaging	Het
Fbxl2	A	T	9: 113,985,306	H272Q	probably benign	Het
Fgd3	C	T	13: 49,273,709		probably null	Het
Fhdc1	C	A	3: 84,444,826	V1031F	probably benign	Het
Fscn1	T	C	5: 142,972,021	Y308H	probably damaging	Het
Gm5878	G	A	6: 85,125,651	R31*	probably null	Het
Gm996	A	G	2: 25,579,108	Y264H	possibly damaging	Het
Gpatch2l	T	C	12: 86,260,679	V277A	probably benign	Het
Greb1l	T	A	18: 10,544,561	M1385K	probably benign	Het
Grin2a	A	G	16: 9,653,589	I605T	possibly damaging	Het
Hoxc11	C	T	15: 102,954,671	S49F	probably damaging	Het
Igf2r	C	T	17: 12,709,511	E982K	possibly damaging	Het
Ighv10-3	A	T	12: 114,523,504	M99K	possibly damaging	Het
Itgb4	A	T	11: 115,988,729	T614S	probably benign	Het
Kcnv1	G	A	15: 45,114,444	T66M	probably damaging	Het
Mast4	A	G	13: 102,774,248	V461A	probably damaging	Het
Mcts2	G	A	2: 152,687,664	V132M	probably damaging	Het
Mical3	C	A	6: 120,934,838	E1083*	probably null	Het
Nbeal2	A	G	9: 110,631,793		probably benign	Het
Nek4	T	C	14: 30,953,906	V66A	probably damaging	Het
Nfasc	A	G	1: 132,631,705	F229S	probably damaging	Het
Nhsl1	T	C	10: 18,526,689	F1221S	probably damaging	Het
Nr1d1	T	G	11: 98,771,814	K118Q	probably damaging	Het
Ntm	T	C	9: 29,109,431	E164G	probably damaging	Het
Olfr576	A	G	7: 102,966,024	N308S	probably benign	Het
Parp1	G	T	1: 180,587,329	A411S	probably benign	Het
Pds5b	A	G	5: 150,800,854	T1301A	probably benign	Het
Pkhd1	A	G	1: 20,058,617	V3954A	probably benign	Het
Pkp4	A	T	2: 59,350,608	K739I	probably damaging	Het
Pla2g4e	T	C	2: 120,186,446		probably benign	Het
Ralgds	T	C	2: 28,552,095	L96P	probably damaging	Het
Rbm6	A	T	9: 107,847,247		probably benign	Het
Scp2d1	T	C	2: 144,824,167	L142P	probably damaging	Het
Setd5	AT	ATT	6: 113,111,320		probably benign	Het
Sgf29	G	A	7: 126,671,777	C143Y	probably damaging	Het
Slc22a12	A	G	19: 6,541,099	I156T	probably benign	Het
Stambpl1	A	G	19: 34,234,046	Q169R	probably benign	Het
Tex2	T	C	11: 106,567,006		probably benign	Het
Trip11	A	T	12: 101,884,316	I878N	probably damaging	Het
Ttf1	C	T	2: 29,065,476	S284L	probably benign	Het
Ttn	A	T	2: 76,811,243	L5176Q	possibly damaging	Het
Ugt2b5	A	T	5: 87,139,723	V195E	probably damaging	Het
Vmn1r14	T	A	6: 57,233,823	Y85N	probably benign	Het
Wdyhv1	T	C	15: 58,152,714	S120P	probably benign	Het
Zfp131	C	T	13: 119,776,018	R268H	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
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

Predicted Primers

PCR Primer
(F):5'- TTCTGGAGATCAAATGTGCTGAAAG -3'
(R):5'- CCAACTGTTCGAGCCACATC -3'

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

Posted On

2015-06-24