Mutagenetix > Incidental Mutation

Incidental Mutation 'R5654:Plod2'

442180

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

043300-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5654 (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 92475876 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 320 (T320A)

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: T320A

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

SMART Domains

Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: T320A

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: T320A

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

SMART Domains

Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: T320A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161906

Meta Mutation Damage Score

0.0665

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.6%
20x: 96.1%

Validation Efficiency

96% (69/72)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb6	T	C	1: 75,151,479 (GRCm39)		probably null	Het
Abcc9	G	A	6: 142,571,371 (GRCm39)		probably benign	Het
Acss2	T	C	2: 155,416,575 (GRCm39)		probably benign	Het
Atp8b4	G	A	2: 126,217,725 (GRCm39)	T597I	probably damaging	Het
Btaf1	A	T	19: 36,961,015 (GRCm39)	N796I	probably benign	Het
Caskin2	T	C	11: 115,690,905 (GRCm39)		probably null	Het
Cdhr2	A	G	13: 54,884,349 (GRCm39)	N1295D	probably benign	Het
Cog3	G	A	14: 75,962,239 (GRCm39)	T534M	probably benign	Het
Cpne1	A	G	2: 155,919,561 (GRCm39)	S303P	probably damaging	Het
Cs	G	A	10: 128,187,086 (GRCm39)	G74S	possibly damaging	Het
Cyb5r4	G	T	9: 86,929,533 (GRCm39)	S229I	probably damaging	Het
Ddr1	C	T	17: 35,997,400 (GRCm39)	A531T	probably benign	Het
Ect2l	C	T	10: 18,018,810 (GRCm39)	V529M	probably damaging	Het
Edaradd	C	A	13: 12,493,161 (GRCm39)	R177L	possibly damaging	Het
Esf1	T	C	2: 140,006,148 (GRCm39)	D333G	possibly damaging	Het
Fam8a1	T	A	13: 46,827,814 (GRCm39)	L334H	probably damaging	Het
Fbxl18	A	G	5: 142,871,558 (GRCm39)	I559T	probably damaging	Het
Fcrl2	A	C	3: 87,164,851 (GRCm39)	V225G	probably benign	Het
Ido1	C	T	8: 25,077,819 (GRCm39)	V83M	probably damaging	Het
Iffo1	T	G	6: 125,130,030 (GRCm39)	C419G	probably damaging	Het
Igfals	A	T	17: 25,100,439 (GRCm39)	Y510F	probably benign	Het
Ipo9	A	T	1: 135,313,210 (GRCm39)	Y1006*	probably null	Het
Itgb4	C	T	11: 115,874,983 (GRCm39)	R447W	probably benign	Het
Jmjd1c	T	A	10: 67,065,785 (GRCm39)	S1737T	probably benign	Het
Klhl32	C	T	4: 24,800,805 (GRCm39)		probably null	Het
Klk1b11	T	A	7: 43,427,810 (GRCm39)	C173S	probably damaging	Het
Klk1b24	A	T	7: 43,840,889 (GRCm39)	M106L	probably benign	Het
Lamp1	G	A	8: 13,221,388 (GRCm39)		probably null	Het
Mapk4	A	T	18: 74,103,365 (GRCm39)	V48E	probably damaging	Het
Marchf6	A	T	15: 31,486,082 (GRCm39)	D395E	probably damaging	Het
Mdp1	A	G	14: 55,896,465 (GRCm39)	F157S	probably damaging	Het
Mettl21e	A	T	1: 44,250,255 (GRCm39)	F50L	probably damaging	Het
Mrgpra2a	A	G	7: 47,077,153 (GRCm39)	I35T	probably benign	Het
Natd1	T	C	11: 60,796,892 (GRCm39)	Y91C	probably damaging	Het
Nbas	T	A	12: 13,633,476 (GRCm39)	Y2294N	probably damaging	Het
Nrcam	A	G	12: 44,610,841 (GRCm39)	T520A	probably benign	Het
Nrf1	A	G	6: 30,117,061 (GRCm39)	T324A	probably benign	Het
Or10a2	G	A	7: 106,673,394 (GRCm39)	A120T	probably damaging	Het
Or4k51	T	A	2: 111,585,326 (GRCm39)	I244N	probably damaging	Het
Or52a5	A	C	7: 103,427,182 (GRCm39)	D123E	probably damaging	Het
Or5m11b	A	G	2: 85,806,500 (GRCm39)	I304M	probably benign	Het
Pam	C	T	1: 97,792,123 (GRCm39)	V433I	probably benign	Het
Pck1	T	A	2: 173,000,353 (GRCm39)	Y595N	probably damaging	Het
Per2	C	T	1: 91,373,223 (GRCm39)		probably null	Het
Piezo2	G	C	18: 63,278,162 (GRCm39)	F247L	possibly damaging	Het
Pkdcc	A	G	17: 83,523,337 (GRCm39)	Y148C	probably damaging	Het
Ppip5k1	G	A	2: 121,147,157 (GRCm39)	R1155C	probably benign	Het
Ppp1r15b	C	T	1: 133,059,382 (GRCm39)		probably benign	Het
Prkn	C	T	17: 11,456,536 (GRCm39)	A119V	probably damaging	Het
Ptprz1	G	T	6: 22,986,133 (GRCm39)	C311F	probably damaging	Het
Rab11fip3	A	T	17: 26,235,038 (GRCm39)	V44E	probably damaging	Het
Rpl5	T	A	5: 108,051,514 (GRCm39)		probably benign	Het
Rttn	G	A	18: 89,066,556 (GRCm39)	V1201I	probably benign	Het
Sdk1	A	G	5: 141,921,853 (GRCm39)	N283S	probably damaging	Het
Shank3	T	A	15: 89,405,529 (GRCm39)	N418K	probably benign	Het
Shmt2	T	C	10: 127,353,668 (GRCm39)	D499G	probably benign	Het
Slc25a46	A	G	18: 31,716,293 (GRCm39)	L403S	probably damaging	Het
Slc5a1	A	G	5: 33,303,955 (GRCm39)	T257A	probably benign	Het
Snrnp35	T	C	5: 124,628,535 (GRCm39)	V116A	probably benign	Het
Spag9	T	A	11: 93,981,538 (GRCm39)	F593I	probably damaging	Het
Tmem171	C	A	13: 98,828,574 (GRCm39)	R192L	probably benign	Het
Trappc3l	T	A	10: 33,978,703 (GRCm39)	L169Q	unknown	Het
Ube2s	T	C	7: 4,811,431 (GRCm39)	E148G	probably damaging	Het
Uspl1	T	C	5: 149,146,521 (GRCm39)	F424S	probably damaging	Het
Vmn1r2	T	C	4: 3,172,261 (GRCm39)	V60A	probably benign	Het
Wdfy4	T	C	14: 32,829,575 (GRCm39)		probably null	Het
Zfp735	C	T	11: 73,602,964 (GRCm39)	S636L	possibly damaging	Het
Zswim9	G	A	7: 12,995,094 (GRCm39)	S354F	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
R1917:Plod2	UTSW	9	92,463,310 (GRCm39)	missense	probably benign
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
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'- GATTATGCTGACTGACATGAAAGTC -3'
(R):5'- TGTCAATTTCACACTGCTCAGC -3'

Sequencing Primer
(F):5'- CTGACTGACATGAAAGTCTAGTGTGC -3'
(R):5'- TCACACTGCTCAGCCTAATATTAG -3'

Posted On

2016-11-09