Mutagenetix > Incidental Mutation

Incidental Mutation 'R1917:Plod2'

212616

Institutional Source

Beutler Lab

Gene Symbol

Plod2

Ensembl Gene

ENSMUSG00000032374

Gene Name

procollagen lysine, 2-oxoglutarate 5-dioxygenase 2

Synonyms

Plod-2, LH2, lysyl hydroxylase 2, D530025C14Rik

MMRRC Submission

039935-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1917 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

92424276-92490481 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 92463310 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 132 (T132A)

Ref Sequence

ENSEMBL: ENSMUSP00000125373 (fasta)

Gene Model

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

AlphaFold

Q9R0B9

Predicted Effect

probably benign
Transcript: ENSMUST00000070522
AA Change: T132A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: T132A

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: T132A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: T132A

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

0.0898

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.8%
20x: 93.6%

Validation Efficiency

100% (83/83)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8a	A	G	11: 109,982,341 (GRCm39)		probably benign	Het
Adgre5	A	G	8: 84,455,738 (GRCm39)	V190A	probably damaging	Het
Akap6	A	G	12: 53,151,395 (GRCm39)	N1153S	probably benign	Het
Aldh1a7	G	A	19: 20,704,819 (GRCm39)	H20Y	probably benign	Het
B430306N03Rik	A	G	17: 48,631,176 (GRCm39)	E278G	probably benign	Het
Cacna1b	C	A	2: 24,506,891 (GRCm39)	R72L	probably null	Het
Cc2d2a	C	G	5: 43,863,564 (GRCm39)	S675R	probably damaging	Het
Ccdc88b	T	A	19: 6,826,594 (GRCm39)	E1040D	probably damaging	Het
Cmtm7	A	G	9: 114,592,432 (GRCm39)	V55A	probably damaging	Het
Coq4	A	C	2: 29,679,938 (GRCm39)	T77P	probably damaging	Het
Cyp2j11	C	A	4: 96,228,211 (GRCm39)	W136L	probably damaging	Het
Dctn2	T	A	10: 127,110,918 (GRCm39)	Y86*	probably null	Het
Ddx56	A	G	11: 6,213,937 (GRCm39)		probably null	Het
Dop1b	T	C	16: 93,513,150 (GRCm39)	S30P	probably damaging	Het
Ep400	T	C	5: 110,851,441 (GRCm39)	K1347R	unknown	Het
Fat3	T	A	9: 15,908,353 (GRCm39)	T2550S	possibly damaging	Het
Fcrla	G	T	1: 170,755,095 (GRCm39)	C5*	probably null	Het
Fem1al	A	G	11: 29,774,039 (GRCm39)	S473P	probably benign	Het
Fermt1	T	A	2: 132,764,762 (GRCm39)	D365V	probably damaging	Het
Fhod3	A	G	18: 25,123,022 (GRCm39)		probably benign	Het
Fhod3	A	G	18: 25,218,658 (GRCm39)	D807G	probably benign	Het
Fnip1	C	T	11: 54,371,510 (GRCm39)	T177I	probably damaging	Het
Gart	T	C	16: 91,425,037 (GRCm39)	Y662C	probably damaging	Het
Gda	A	T	19: 21,375,004 (GRCm39)		probably benign	Het
Gk	A	G	X: 84,804,186 (GRCm39)	I85T	probably damaging	Het
Gm3476	A	G	14: 6,118,358 (GRCm38)	L255P	possibly damaging	Het
Gm9966	T	C	7: 95,607,684 (GRCm39)	C2R	unknown	Het
Gnpda1	T	C	18: 38,466,243 (GRCm39)		probably null	Het
Gtf2h4	G	A	17: 35,981,090 (GRCm39)	L246F	possibly damaging	Het
Hao1	A	T	2: 134,364,980 (GRCm39)	S216T	probably benign	Het
Hnrnpr	C	A	4: 136,059,799 (GRCm39)	S301*	probably null	Het
Hsd3b2	A	G	3: 98,619,342 (GRCm39)	I201T	probably benign	Het
Jade2	T	C	11: 51,709,365 (GRCm39)	E548G	possibly damaging	Het
Katnbl1	T	C	2: 112,239,524 (GRCm39)	I241T	probably benign	Het
Keap1	G	T	9: 21,145,102 (GRCm39)	Q299K	probably benign	Het
Kif1a	T	C	1: 92,946,753 (GRCm39)	I1650V	possibly damaging	Het
Lrba	G	A	3: 86,571,808 (GRCm39)	G275R	probably damaging	Het
Map3k9	C	A	12: 81,827,564 (GRCm39)	E29*	probably null	Het
Mat1a	G	A	14: 40,843,394 (GRCm39)	V307I	probably damaging	Het
Mcm2	A	T	6: 88,868,785 (GRCm39)	M324K	possibly damaging	Het
Metap1d	T	C	2: 71,341,871 (GRCm39)	V155A	probably damaging	Het
Mtbp	A	G	15: 55,428,073 (GRCm39)		probably benign	Het
Myh14	T	C	7: 44,307,349 (GRCm39)	T231A	probably benign	Het
Mylk4	A	T	13: 32,908,836 (GRCm39)	D90E	probably benign	Het
Myo15b	T	A	11: 115,773,080 (GRCm39)	I1837K	possibly damaging	Het
Myo3a	T	A	2: 22,296,733 (GRCm39)	H242Q	probably damaging	Het
Nxn	A	G	11: 76,152,498 (GRCm39)		probably benign	Het
Or6c2	T	A	10: 129,362,918 (GRCm39)	V274D	probably damaging	Het
Pak3	C	A	X: 142,574,298 (GRCm39)	A553E	possibly damaging	Het
Pdia2	T	A	17: 26,417,079 (GRCm39)	T122S	possibly damaging	Het
Pira12	C	T	7: 3,900,637 (GRCm39)	V38M	probably damaging	Het
Ptprz1	T	A	6: 23,035,039 (GRCm39)		probably benign	Het
Rad54b	A	C	4: 11,601,693 (GRCm39)	N416T	probably damaging	Het
Recql4	A	T	15: 76,588,037 (GRCm39)	Y1142*	probably null	Het
Rnf216	A	G	5: 142,978,561 (GRCm39)	V859A	probably benign	Het
Scnm1	G	T	3: 95,037,584 (GRCm39)	P161T	possibly damaging	Het
Serpinb6b	A	G	13: 33,162,223 (GRCm39)	I222V	probably benign	Het
Serpinf1	A	G	11: 75,301,833 (GRCm39)	I274T	possibly damaging	Het
Slc28a1	T	C	7: 80,819,334 (GRCm39)	F641L	probably benign	Het
Slc8a2	A	G	7: 15,886,845 (GRCm39)	I657V	probably benign	Het
Smchd1	A	G	17: 71,714,232 (GRCm39)	I877T	possibly damaging	Het
Spata31	T	C	13: 65,068,679 (GRCm39)	Y276H	possibly damaging	Het
Spire2	A	G	8: 124,089,810 (GRCm39)	D447G	probably benign	Het
Stk3	G	A	15: 35,073,363 (GRCm39)	T119I	probably damaging	Het
Stxbp5	C	A	10: 9,688,042 (GRCm39)	V420F	possibly damaging	Het
Sult2a5	T	C	7: 13,404,609 (GRCm39)	F282S	probably damaging	Het
Syk	A	T	13: 52,776,744 (GRCm39)	D248V	probably damaging	Het
Thoc6	C	T	17: 23,888,364 (GRCm39)		probably benign	Het
Timd5	A	G	11: 46,419,358 (GRCm39)	D58G	possibly damaging	Het
Tll2	T	A	19: 41,116,936 (GRCm39)	D293V	possibly damaging	Het
Umodl1	G	A	17: 31,203,017 (GRCm39)	V457M	probably damaging	Het
Usp19	T	A	9: 108,376,524 (GRCm39)	C689*	probably null	Het
Usp24	T	G	4: 106,267,483 (GRCm39)	V1955G	probably damaging	Het
Vmn1r226	T	C	17: 20,907,842 (GRCm39)	S25P	probably damaging	Het
Vmn2r69	C	T	7: 85,060,891 (GRCm39)	C231Y	probably damaging	Het
Wdr73	C	T	7: 80,543,081 (GRCm39)	D176N	probably benign	Het
Wnt7b	T	A	15: 85,443,281 (GRCm39)	I41F	probably damaging	Het
Zfhx3	T	C	8: 109,682,880 (GRCm39)	S3440P	unknown	Het
Zfp52	T	G	17: 21,780,426 (GRCm39)	N91K	probably benign	Het
Zfp930	C	A	8: 69,681,357 (GRCm39)	Q350K	probably benign	Het
Zfp949	T	C	9: 88,452,115 (GRCm39)	S562P	probably damaging	Het

Other mutations in Plod2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00715:Plod2	APN	9	92,480,667 (GRCm39)	missense	probably damaging	0.99
IGL00945:Plod2	APN	9	92,466,549 (GRCm39)	missense	probably benign	0.08
IGL01386:Plod2	APN	9	92,488,655 (GRCm39)	missense	probably damaging	0.99
IGL01519:Plod2	APN	9	92,477,348 (GRCm39)	missense	probably benign	0.00
IGL01836:Plod2	APN	9	92,488,551 (GRCm39)	splice site	probably benign
IGL02490:Plod2	APN	9	92,468,895 (GRCm39)	missense	probably benign	0.00
IGL02496:Plod2	APN	9	92,489,147 (GRCm39)	missense	probably damaging	1.00
IGL02699:Plod2	APN	9	92,489,195 (GRCm39)	missense	probably damaging	1.00
IGL02735:Plod2	APN	9	92,477,442 (GRCm39)	splice site	probably benign
IGL03106:Plod2	APN	9	92,455,620 (GRCm39)	missense	probably damaging	0.98
R0270:Plod2	UTSW	9	92,466,574 (GRCm39)	missense	probably benign	0.10
R0546:Plod2	UTSW	9	92,477,388 (GRCm39)	missense	probably damaging	1.00
R0589:Plod2	UTSW	9	92,475,799 (GRCm39)	missense	probably benign
R0707:Plod2	UTSW	9	92,487,480 (GRCm39)	missense	possibly damaging	0.91
R1491:Plod2	UTSW	9	92,488,637 (GRCm39)	missense	probably benign	0.00
R1572:Plod2	UTSW	9	92,485,120 (GRCm39)	splice site	probably benign
R1731:Plod2	UTSW	9	92,466,657 (GRCm39)	critical splice donor site	probably null
R1895:Plod2	UTSW	9	92,489,188 (GRCm39)	missense	probably damaging	1.00
R1946:Plod2	UTSW	9	92,489,188 (GRCm39)	missense	probably damaging	1.00
R3850:Plod2	UTSW	9	92,424,598 (GRCm39)	missense	probably benign	0.28
R3973:Plod2	UTSW	9	92,480,672 (GRCm39)	nonsense	probably null
R3974:Plod2	UTSW	9	92,480,672 (GRCm39)	nonsense	probably null
R4289:Plod2	UTSW	9	92,485,041 (GRCm39)	missense	possibly damaging	0.89
R4423:Plod2	UTSW	9	92,484,042 (GRCm39)	missense	probably benign	0.00
R4647:Plod2	UTSW	9	92,487,503 (GRCm39)	nonsense	probably null
R4754:Plod2	UTSW	9	92,488,584 (GRCm39)	nonsense	probably null
R4769:Plod2	UTSW	9	92,477,325 (GRCm39)	missense	probably damaging	1.00
R5279:Plod2	UTSW	9	92,463,376 (GRCm39)	missense	probably damaging	1.00
R5535:Plod2	UTSW	9	92,488,622 (GRCm39)	missense	probably damaging	1.00
R5654:Plod2	UTSW	9	92,475,876 (GRCm39)	missense	probably benign
R5764:Plod2	UTSW	9	92,485,074 (GRCm39)	missense	probably damaging	0.97
R5885:Plod2	UTSW	9	92,488,709 (GRCm39)	critical splice donor site	probably null
R5940:Plod2	UTSW	9	92,473,450 (GRCm39)	missense	probably benign	0.39
R6917:Plod2	UTSW	9	92,475,823 (GRCm39)	missense	possibly damaging	0.87
R7109:Plod2	UTSW	9	92,455,650 (GRCm39)	missense	probably damaging	1.00
R7221:Plod2	UTSW	9	92,466,580 (GRCm39)	missense	probably damaging	1.00
R7311:Plod2	UTSW	9	92,466,611 (GRCm39)	missense	probably damaging	1.00
R7963:Plod2	UTSW	9	92,487,499 (GRCm39)	missense	probably benign	0.07
R8205:Plod2	UTSW	9	92,424,371 (GRCm39)	start gained	probably benign
R8794:Plod2	UTSW	9	92,482,801 (GRCm39)	missense	probably damaging	0.98
R8873:Plod2	UTSW	9	92,489,112 (GRCm39)	intron	probably benign
R9044:Plod2	UTSW	9	92,489,273 (GRCm39)	missense	probably damaging	0.97
R9071:Plod2	UTSW	9	92,485,048 (GRCm39)	missense	probably benign	0.09
R9120:Plod2	UTSW	9	92,424,380 (GRCm39)	start gained	probably benign
Z1088:Plod2	UTSW	9	92,485,088 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CAAATGTAGTTCCTGTGATGTGAG -3'
(R):5'- AGCGCTAACCTGTGAGTGAG -3'

Sequencing Primer
(F):5'- GGTTGCCTGCTGTGTTCTCTAAAC -3'
(R):5'- CTAACCTGTGAGTGAGCTTTCAG -3'

Posted On

2014-07-14