Mutagenetix > Incidental Mutation

Incidental Mutation 'R0270:Plod2'

186140

Institutional Source

Beutler Lab

Gene Symbol

Plod2

Ensembl Gene

ENSMUSG00000032374

Gene Name

procollagen lysine, 2-oxoglutarate 5-dioxygenase 2

Synonyms

D530025C14Rik, Plod-2, LH2, lysyl hydroxylase 2

MMRRC Submission

038496-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0270 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

92542223-92608428 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 92584521 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 178 (R178L)

Ref Sequence

ENSEMBL: ENSMUSP00000068611 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070522] [ENSMUST00000160359]

AlphaFold

Q9R0B9

Predicted Effect

probably benign
Transcript: ENSMUST00000070522
AA Change: R178L

PolyPhen 2 Score 0.100 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: R178L

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
low complexity region	181	193	N/A	INTRINSIC
low complexity region	307	321	N/A	INTRINSIC
Blast:P4Hc	453	500	1e-22	BLAST
P4Hc	563	736	6.38e-21	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160142

Predicted Effect

probably benign
Transcript: ENSMUST00000160359
AA Change: R178L

PolyPhen 2 Score 0.047 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: R178L

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
low complexity region	181	193	N/A	INTRINSIC
low complexity region	307	321	N/A	INTRINSIC
Blast:P4Hc	453	500	1e-22	BLAST
P4Hc	584	757	6.38e-21	SMART

Meta Mutation Damage Score

0.3307

Coding Region Coverage

1x: 98.7%
3x: 97.7%
10x: 96.0%
20x: 93.2%

Validation Efficiency

99% (113/114)

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. Mutations in the coding region of this gene are associated with Bruck syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 109 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110009E18Rik	T	A	1: 120,166,176 (GRCm38)		probably benign	Het
4922502D21Rik	A	T	6: 129,325,608 (GRCm38)	L152*	probably null	Het
Abcf3	T	A	16: 20,560,168 (GRCm38)		probably null	Het
Acadm	C	T	3: 153,936,324 (GRCm38)	M190I	possibly damaging	Het
Adamtsl3	G	A	7: 82,556,824 (GRCm38)	R739Q	probably damaging	Het
Ank1	T	A	8: 23,088,925 (GRCm38)		probably benign	Het
Ap3b1	T	A	13: 94,404,118 (GRCm38)		probably benign	Het
Arhgdib	A	G	6: 136,926,734 (GRCm38)	V31A	probably damaging	Het
Arid4a	A	G	12: 71,072,632 (GRCm38)	R342G	probably damaging	Het
Asic3	C	T	5: 24,417,702 (GRCm38)	L517F	probably benign	Het
Atxn7l1	C	T	12: 33,342,151 (GRCm38)	P242L	possibly damaging	Het
AY761185	T	A	8: 20,944,600 (GRCm38)	E37D	possibly damaging	Het
Babam1	T	A	8: 71,398,406 (GRCm38)	D104E	probably damaging	Het
Batf	A	T	12: 85,708,672 (GRCm38)	T100S	probably benign	Het
Blcap	A	T	2: 157,557,977 (GRCm38)	Y59*	probably null	Het
Cacnb3	G	A	15: 98,642,559 (GRCm38)	A350T	probably damaging	Het
Cdk15	T	A	1: 59,310,806 (GRCm38)	V319D	probably damaging	Het
Cenpf	T	C	1: 189,650,714 (GRCm38)	H2661R	probably benign	Het
Cenpq	T	C	17: 40,930,050 (GRCm38)	E106G	probably damaging	Het
Cfap43	A	G	19: 47,797,203 (GRCm38)		probably benign	Het
Cfb	G	A	17: 34,860,386 (GRCm38)	S778L	possibly damaging	Het
Clspn	T	A	4: 126,573,236 (GRCm38)	N631K	probably damaging	Het
Cntn2	T	A	1: 132,521,724 (GRCm38)	T660S	probably damaging	Het
Cntrob	T	A	11: 69,311,341 (GRCm38)	H475L	possibly damaging	Het
Ddx46	T	C	13: 55,674,104 (GRCm38)	I863T	probably benign	Het
Dnah11	G	A	12: 118,041,013 (GRCm38)	T2191I	probably damaging	Het
Dock9	T	C	14: 121,575,999 (GRCm38)	T1703A	probably benign	Het
Fam13c	C	T	10: 70,544,513 (GRCm38)	P424S	probably benign	Het
Fan1	T	C	7: 64,348,871 (GRCm38)	N968D	probably benign	Het
Fbxl20	A	T	11: 98,098,503 (GRCm38)		probably benign	Het
Fkbp1b	A	T	12: 4,838,229 (GRCm38)		probably benign	Het
G930045G22Rik	T	A	6: 50,847,059 (GRCm38)		noncoding transcript	Het
Gm28042	C	A	2: 120,041,592 (GRCm38)	R1008S	probably benign	Het
Gm6614	T	A	6: 141,972,411 (GRCm38)	I580F	possibly damaging	Het
Gm8298	T	A	3: 59,877,019 (GRCm38)	N304K	probably benign	Het
Gon4l	G	A	3: 88,858,400 (GRCm38)	S376N	probably damaging	Het
Gstt3	C	A	10: 75,780,915 (GRCm38)	R15L	probably damaging	Het
Gtdc1	A	T	2: 44,752,174 (GRCm38)	S73T	possibly damaging	Het
H2afy	G	A	13: 56,096,114 (GRCm38)		probably benign	Het
Hhatl	A	G	9: 121,784,720 (GRCm38)	S419P	probably benign	Het
Hirip3	T	G	7: 126,863,191 (GRCm38)	S46R	probably damaging	Het
Hsf2	A	G	10: 57,502,639 (GRCm38)	T204A	probably benign	Het
Impg2	G	A	16: 56,269,015 (GRCm38)	E1108K	possibly damaging	Het
Itgb2l	G	T	16: 96,422,930 (GRCm38)		probably benign	Het
Itih5	A	T	2: 10,251,264 (GRCm38)	N847I	probably benign	Het
Kif1a	T	C	1: 93,054,442 (GRCm38)		probably benign	Het
Klhl1	T	A	14: 96,518,344 (GRCm38)		probably benign	Het
Ktn1	T	A	14: 47,714,662 (GRCm38)	D963E	probably benign	Het
Lclat1	T	A	17: 73,240,027 (GRCm38)	V313E	probably benign	Het
Lrrn4	T	C	2: 132,870,719 (GRCm38)	S395G	probably benign	Het
Mbtps1	G	A	8: 119,538,117 (GRCm38)		probably benign	Het
Me1	A	G	9: 86,596,204 (GRCm38)		probably benign	Het
Mov10	C	A	3: 104,795,405 (GRCm38)	C948F	probably benign	Het
Mterf1a	G	A	5: 3,890,990 (GRCm38)	Q293*	probably null	Het
Nfkb2	A	T	19: 46,311,626 (GRCm38)	M838L	possibly damaging	Het
Nhlrc2	T	A	19: 56,551,870 (GRCm38)	L97Q	probably damaging	Het
Nr6a1	A	T	2: 38,739,020 (GRCm38)	Y331N	possibly damaging	Het
Nup214	C	T	2: 32,034,814 (GRCm38)	A1785V	probably damaging	Het
Ogg1	C	T	6: 113,329,256 (GRCm38)	T138I	probably benign	Het
Olfr1461	A	G	19: 13,165,887 (GRCm38)	Y291C	probably damaging	Het
Olfr1489	A	G	19: 13,633,684 (GRCm38)	Y191C	probably damaging	Het
Olfr202	A	G	16: 59,283,753 (GRCm38)	V248A	probably damaging	Het
Olfr829	T	A	9: 18,856,831 (GRCm38)	Y60N	probably damaging	Het
Polr3b	T	A	10: 84,718,475 (GRCm38)	L1017Q	probably benign	Het
Postn	C	A	3: 54,384,550 (GRCm38)	T724N	probably damaging	Het
Ppm1l	T	G	3: 69,317,976 (GRCm38)		probably benign	Het
Prpf8	T	G	11: 75,505,249 (GRCm38)	L1983R	probably damaging	Het
Psma7	A	G	2: 180,039,400 (GRCm38)	V59A	probably benign	Het
Qser1	T	A	2: 104,788,961 (GRCm38)	Y502F	probably benign	Het
Rad50	T	C	11: 53,668,025 (GRCm38)	D1129G	probably damaging	Het
Rasal1	C	A	5: 120,674,729 (GRCm38)	P606Q	probably damaging	Het
Rgs6	A	G	12: 83,133,689 (GRCm38)	Y438C	probably damaging	Het
Rnf180	A	G	13: 105,252,266 (GRCm38)	C73R	probably benign	Het
Rnf216	T	A	5: 143,080,241 (GRCm38)	I474F	possibly damaging	Het
Sdha	A	T	13: 74,332,247 (GRCm38)	L371Q	probably damaging	Het
Sdk1	T	G	5: 142,084,566 (GRCm38)	L1162R	possibly damaging	Het
Sh3rf2	T	C	18: 42,104,081 (GRCm38)	I223T	probably damaging	Het
Sirpb1a	A	G	3: 15,410,527 (GRCm38)	V316A	probably damaging	Het
Slc12a4	A	T	8: 105,945,389 (GRCm38)	I897N	probably benign	Het
Slc35d1	A	T	4: 103,190,838 (GRCm38)	V243E	probably damaging	Het
Slc4a11	T	A	2: 130,690,932 (GRCm38)	K200N	possibly damaging	Het
Slc9a8	T	A	2: 167,451,296 (GRCm38)	M188K	probably damaging	Het
Snrnp200	T	C	2: 127,232,982 (GRCm38)	S1492P	probably damaging	Het
Sphk2	T	C	7: 45,710,725 (GRCm38)	*618W	probably null	Het
Sytl2	T	C	7: 90,403,020 (GRCm38)		probably benign	Het
Tdpoz3	A	G	3: 93,826,924 (GRCm38)	N302S	probably benign	Het
Tdrd6	T	C	17: 43,624,308 (GRCm38)	M1950V	probably benign	Het
Tmem39a	A	G	16: 38,564,313 (GRCm38)		probably benign	Het
Trip4	A	T	9: 65,858,358 (GRCm38)	I353K	probably damaging	Het
Trip6	A	T	5: 137,312,841 (GRCm38)	F204L	probably benign	Het
Trpm4	T	A	7: 45,319,253 (GRCm38)	I419F	possibly damaging	Het
Ttn	C	A	2: 76,944,796 (GRCm38)	E1967D	probably damaging	Het
Uba2	C	T	7: 34,150,856 (GRCm38)	V391M	possibly damaging	Het
Ubr4	T	G	4: 139,479,435 (GRCm38)		probably benign	Het
Upf1	G	A	8: 70,335,645 (GRCm38)		probably benign	Het
Vmn1r228	A	C	17: 20,776,596 (GRCm38)	V220G	possibly damaging	Het
Vmn2r79	A	G	7: 87,003,386 (GRCm38)	M429V	probably benign	Het
Vps36	C	T	8: 22,210,456 (GRCm38)	T210I	possibly damaging	Het
Wdr17	C	T	8: 54,693,096 (GRCm38)	A90T	possibly damaging	Het
Ybx1	C	T	4: 119,281,591 (GRCm38)	G126D	probably benign	Het
Yipf5	C	A	18: 40,206,407 (GRCm38)		probably benign	Het
Zdhhc5	A	C	2: 84,690,115 (GRCm38)	S573A	probably benign	Het
Zfp457	A	T	13: 67,293,927 (GRCm38)	C99S	probably damaging	Het
Zfp52	T	A	17: 21,561,302 (GRCm38)	C471S	probably damaging	Het
Zfp558	C	T	9: 18,467,956 (GRCm38)	V71I	probably damaging	Het
Zfp651	A	G	9: 121,767,575 (GRCm38)	T666A	probably benign	Het
Zfp655	A	G	5: 145,244,457 (GRCm38)	Y375C	probably damaging	Het
Zfp882	A	T	8: 71,914,615 (GRCm38)	T429S	probably benign	Het
Zmym2	T	C	14: 56,949,684 (GRCm38)		probably null	Het

Other mutations in Plod2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00715:Plod2	APN	9	92,598,614 (GRCm38)	missense	probably damaging	0.99
IGL00945:Plod2	APN	9	92,584,496 (GRCm38)	missense	probably benign	0.08
IGL01386:Plod2	APN	9	92,606,602 (GRCm38)	missense	probably damaging	0.99
IGL01519:Plod2	APN	9	92,595,295 (GRCm38)	missense	probably benign	0.00
IGL01836:Plod2	APN	9	92,606,498 (GRCm38)	splice site	probably benign
IGL02490:Plod2	APN	9	92,586,842 (GRCm38)	missense	probably benign	0.00
IGL02496:Plod2	APN	9	92,607,094 (GRCm38)	missense	probably damaging	1.00
IGL02699:Plod2	APN	9	92,607,142 (GRCm38)	missense	probably damaging	1.00
IGL02735:Plod2	APN	9	92,595,389 (GRCm38)	splice site	probably benign
IGL03106:Plod2	APN	9	92,573,567 (GRCm38)	missense	probably damaging	0.98
R0546:Plod2	UTSW	9	92,595,335 (GRCm38)	missense	probably damaging	1.00
R0589:Plod2	UTSW	9	92,593,746 (GRCm38)	missense	probably benign
R0707:Plod2	UTSW	9	92,605,427 (GRCm38)	missense	possibly damaging	0.91
R1491:Plod2	UTSW	9	92,606,584 (GRCm38)	missense	probably benign	0.00
R1572:Plod2	UTSW	9	92,603,067 (GRCm38)	splice site	probably benign
R1731:Plod2	UTSW	9	92,584,604 (GRCm38)	critical splice donor site	probably null
R1895:Plod2	UTSW	9	92,607,135 (GRCm38)	missense	probably damaging	1.00
R1917:Plod2	UTSW	9	92,581,257 (GRCm38)	missense	probably benign
R1946:Plod2	UTSW	9	92,607,135 (GRCm38)	missense	probably damaging	1.00
R3850:Plod2	UTSW	9	92,542,545 (GRCm38)	missense	probably benign	0.28
R3973:Plod2	UTSW	9	92,598,619 (GRCm38)	nonsense	probably null
R3974:Plod2	UTSW	9	92,598,619 (GRCm38)	nonsense	probably null
R4289:Plod2	UTSW	9	92,602,988 (GRCm38)	missense	possibly damaging	0.89
R4423:Plod2	UTSW	9	92,601,989 (GRCm38)	missense	probably benign	0.00
R4647:Plod2	UTSW	9	92,605,450 (GRCm38)	nonsense	probably null
R4754:Plod2	UTSW	9	92,606,531 (GRCm38)	nonsense	probably null
R4769:Plod2	UTSW	9	92,595,272 (GRCm38)	missense	probably damaging	1.00
R5279:Plod2	UTSW	9	92,581,323 (GRCm38)	missense	probably damaging	1.00
R5535:Plod2	UTSW	9	92,606,569 (GRCm38)	missense	probably damaging	1.00
R5654:Plod2	UTSW	9	92,593,823 (GRCm38)	missense	probably benign
R5764:Plod2	UTSW	9	92,603,021 (GRCm38)	missense	probably damaging	0.97
R5885:Plod2	UTSW	9	92,606,656 (GRCm38)	critical splice donor site	probably null
R5940:Plod2	UTSW	9	92,591,397 (GRCm38)	missense	probably benign	0.39
R6917:Plod2	UTSW	9	92,593,770 (GRCm38)	missense	possibly damaging	0.87
R7109:Plod2	UTSW	9	92,573,597 (GRCm38)	missense	probably damaging	1.00
R7221:Plod2	UTSW	9	92,584,527 (GRCm38)	missense	probably damaging	1.00
R7311:Plod2	UTSW	9	92,584,558 (GRCm38)	missense	probably damaging	1.00
R7963:Plod2	UTSW	9	92,605,446 (GRCm38)	missense	probably benign	0.07
R8205:Plod2	UTSW	9	92,542,318 (GRCm38)	start gained	probably benign
R8794:Plod2	UTSW	9	92,600,748 (GRCm38)	missense	probably damaging	0.98
R8873:Plod2	UTSW	9	92,607,059 (GRCm38)	intron	probably benign
R9044:Plod2	UTSW	9	92,607,220 (GRCm38)	missense	probably damaging	0.97
R9071:Plod2	UTSW	9	92,602,995 (GRCm38)	missense	probably benign	0.09
R9120:Plod2	UTSW	9	92,542,327 (GRCm38)	start gained	probably benign
Z1088:Plod2	UTSW	9	92,603,035 (GRCm38)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CGTTAGACCTCATGACTTCCCAGC -3'
(R):5'- CTCCAGTCTCAGAAACGTTACTGCC -3'

Sequencing Primer
(F):5'- ATGACTTCCCAGCATTGTCAG -3'
(R):5'- GTGATGGGACCCACATAATTTGC -3'

Posted On

2014-05-08