Mutagenetix > Incidental Mutation

Incidental Mutation 'R7221:Plod2'

561825

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

045293-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7221 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

92424276-92490481 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 92466580 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 180 (V180A)

Ref Sequence

ENSEMBL: ENSMUSP00000125373 (fasta)

Gene Model

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

AlphaFold

Q9R0B9

Predicted Effect

probably damaging
Transcript: ENSMUST00000070522
AA Change: V180A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: V180A

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

probably damaging
Transcript: ENSMUST00000160359
AA Change: V180A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: V180A

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

0.2917

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (77/77)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl2fm1	A	G	3: 59,836,354 (GRCm39)		probably benign	Het
Abr	A	C	11: 76,313,987 (GRCm39)	M720R	probably benign	Het
Acad10	G	A	5: 121,768,273 (GRCm39)	T761M	probably damaging	Het
Agxt	G	T	1: 93,065,623 (GRCm39)	G164V	possibly damaging	Het
Ankar	C	T	1: 72,689,390 (GRCm39)	G1247D	probably damaging	Het
Bptf	A	C	11: 106,945,658 (GRCm39)	L2527R	probably damaging	Het
Brinp2	T	C	1: 158,094,117 (GRCm39)	H195R	possibly damaging	Het
Cacna2d4	G	T	6: 119,213,624 (GRCm39)	R14S	probably benign	Het
Cep126	A	T	9: 8,100,988 (GRCm39)	C515*	probably null	Het
Chia1	A	T	3: 106,039,236 (GRCm39)	N442I	probably damaging	Het
Clasp2	A	G	9: 113,681,825 (GRCm39)	D327G	probably damaging	Het
Cnbd2	T	C	2: 156,215,581 (GRCm39)	F519L	probably benign	Het
Cntrl	T	A	2: 35,041,869 (GRCm39)	F1214I	possibly damaging	Het
Cul9	A	T	17: 46,839,491 (GRCm39)	M829K	probably damaging	Het
Cyp4b1	T	C	4: 115,493,175 (GRCm39)	Q223R	possibly damaging	Het
Defb37	A	T	8: 19,040,988 (GRCm39)	M1K	probably null	Het
Dnah7c	A	T	1: 46,494,937 (GRCm39)	Q55L	possibly damaging	Het
Efcab3	A	G	11: 104,791,432 (GRCm39)	N2882S	probably benign	Het
Eif2b4	A	T	5: 31,345,131 (GRCm39)	D463E	possibly damaging	Het
Elapor1	T	G	3: 108,382,317 (GRCm39)	D232A	possibly damaging	Het
Elovl1	C	T	4: 118,288,811 (GRCm39)	H167Y	probably damaging	Het
Emb	T	A	13: 117,404,013 (GRCm39)	L255Q	probably damaging	Het
Eogt	T	C	6: 97,089,685 (GRCm39)	Y465C	probably damaging	Het
Erc2	A	G	14: 27,375,115 (GRCm39)	H111R	probably damaging	Het
Fam234b	T	C	6: 135,205,529 (GRCm39)	F498S	probably damaging	Het
Fgfr3	GAGGCTGGCAGCGTGTACGCAGGC	GAGGC	5: 33,890,092 (GRCm39)		probably null	Het
Flrt3	T	A	2: 140,503,090 (GRCm39)	E179D	probably damaging	Het
Fndc3a	T	C	14: 72,793,597 (GRCm39)	R993G	probably benign	Het
Gm14325	T	C	2: 177,476,403 (GRCm39)	T14A	probably damaging	Het
Gm5464	T	A	14: 67,106,681 (GRCm39)	V106D	unknown	Het
Gpatch11	T	A	17: 79,149,546 (GRCm39)	I182N	possibly damaging	Het
Grm6	A	G	11: 50,753,870 (GRCm39)	R725G	probably damaging	Het
Hap1	A	T	11: 100,239,655 (GRCm39)	M588K	probably benign	Het
Icam2	A	G	11: 106,273,268 (GRCm39)	F15L	probably benign	Het
Ints8	A	G	4: 11,225,613 (GRCm39)	M648T	probably benign	Het
Ipo11	A	T	13: 107,029,065 (GRCm39)	L296Q	probably damaging	Het
Kirrel1	G	A	3: 86,993,704 (GRCm39)	Q518*	probably null	Het
Krt18	G	T	15: 101,937,967 (GRCm39)	D155Y	possibly damaging	Het
Lctl	A	T	9: 64,026,217 (GRCm39)	K91*	probably null	Het
Marf1	C	A	16: 13,960,349 (GRCm39)	R565L	probably damaging	Het
Med13	A	T	11: 86,178,921 (GRCm39)	D1458E	probably benign	Het
Mroh8	T	A	2: 157,071,837 (GRCm39)	Y556F	probably benign	Het
Muc16	C	T	9: 18,553,495 (GRCm39)	G4266D	probably benign	Het
Nsrp1	A	T	11: 76,939,249 (GRCm39)	F182I	probably damaging	Het
Obox3	A	T	7: 15,359,983 (GRCm39)	Y229N	probably benign	Het
Or11h7	A	T	14: 50,891,528 (GRCm39)	Y278F	probably damaging	Het
Or2b2	T	C	13: 21,887,272 (GRCm39)	S34P	probably damaging	Het
Or2b4	A	G	17: 38,116,452 (GRCm39)	K139E	probably benign	Het
Or4a74	T	C	2: 89,440,272 (GRCm39)	Y58C	probably damaging	Het
Or4c108	A	G	2: 88,803,497 (GRCm39)	V246A	probably damaging	Het
Or4p22	T	A	2: 88,317,973 (GRCm39)	V299D	probably damaging	Het
Or8d1	A	G	9: 38,766,538 (GRCm39)	Y60C	probably damaging	Het
Pabpc2	T	A	18: 39,906,963 (GRCm39)	V76D	possibly damaging	Het
Parp9	T	C	16: 35,774,071 (GRCm39)	W348R	probably benign	Het
Pdp1	T	C	4: 11,961,004 (GRCm39)	T455A	probably damaging	Het
Phactr2	A	C	10: 13,122,783 (GRCm39)	D446E	possibly damaging	Het
Pi4kb	T	C	3: 94,901,500 (GRCm39)	L389P	probably damaging	Het
Pla2g4f	C	T	2: 120,131,476 (GRCm39)	R749H	probably benign	Het
Plec	A	G	15: 76,059,974 (GRCm39)	V3321A	probably damaging	Het
Plppr5	A	G	3: 117,414,618 (GRCm39)	I80V	probably damaging	Het
Potefam3d	T	G	8: 69,975,316 (GRCm39)	D50A	probably benign	Het
Rubcn	T	C	16: 32,687,293 (GRCm39)		probably null	Het
Sacs	T	C	14: 61,446,255 (GRCm39)	V2767A	probably damaging	Het
Selenbp2	C	G	3: 94,611,133 (GRCm39)	Y414*	probably null	Het
Slc45a4	A	T	15: 73,458,259 (GRCm39)	M430K	probably benign	Het
Smg1	A	G	7: 117,782,020 (GRCm39)	L1145P	possibly damaging	Het
Spns2	A	G	11: 72,347,742 (GRCm39)	V316A	probably benign	Het
Srl	T	A	16: 4,300,811 (GRCm39)	E753D	probably damaging	Het
Thada	T	C	17: 84,771,794 (GRCm39)	T23A	possibly damaging	Het
Tmem231	T	C	8: 112,660,308 (GRCm39)	T31A	probably benign	Het
Tpr	C	T	1: 150,321,929 (GRCm39)	T2321M	possibly damaging	Het
Ttn	T	A	2: 76,772,195 (GRCm39)	N2615I	unknown	Het
Vmn1r41	A	G	6: 89,724,034 (GRCm39)	I192V	probably benign	Het
Vmn2r83	A	T	10: 79,316,001 (GRCm39)	T466S	probably benign	Het
Vnn1	A	G	10: 23,770,952 (GRCm39)	D60G	probably benign	Het
Wiz	G	A	17: 32,578,139 (GRCm39)	P449S	probably benign	Het
Zic1	A	G	9: 91,246,785 (GRCm39)	S96P	probably damaging	Het
Zw10	T	A	9: 48,981,012 (GRCm39)	S471T	probably benign	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
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
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'- ATCATCTCTCCGTTAAAGCATACC -3'
(R):5'- TTTCTAACTGTGATGGGACCCAC -3'

Sequencing Primer
(F):5'- ACCTACTGATACGTTAGACCTCATG -3'
(R):5'- CTGTGATGGGACCCACATAATTTGC -3'

Posted On

2019-06-26