Mutagenetix > Incidental Mutation

Incidental Mutation 'R7311:Plod2'

567595

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

045367-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7311 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

92542223-92608428 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 92584558 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 190 (D190E)

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: D190E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: D190E

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: D190E

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

SMART Domains

Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: D190E

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001K19Rik	A	G	12: 110,668,750 (GRCm38)	V118A	probably benign	Het
Accsl	C	T	2: 93,865,815 (GRCm38)	G146D	possibly damaging	Het
Acsm1	A	T	7: 119,638,082 (GRCm38)	H206L	probably damaging	Het
Acta2	A	G	19: 34,241,786 (GRCm38)	Y339H	probably damaging	Het
Adcy2	T	C	13: 68,630,954 (GRCm38)	D989G	probably damaging	Het
Ahnak	A	G	19: 9,009,827 (GRCm38)	D2825G	possibly damaging	Het
Ahnak	G	A	19: 9,002,143 (GRCm38)	A264T	probably benign	Het
Akt1	G	T	12: 112,657,153 (GRCm38)	T291K	probably damaging	Het
Arhgap24	A	G	5: 102,892,685 (GRCm38)	D589G	probably damaging	Het
B4galnt3	G	A	6: 120,215,435 (GRCm38)	Q447*	probably null	Het
BC024063	C	T	10: 82,110,159 (GRCm38)	R538C	possibly damaging	Het
Bod1l	A	G	5: 41,794,333 (GRCm38)	S2912P	possibly damaging	Het
Bysl	A	G	17: 47,601,785 (GRCm38)	V360A	possibly damaging	Het
C1qb	A	G	4: 136,880,566 (GRCm38)	V162A	possibly damaging	Het
Ccdc57	G	A	11: 120,873,741 (GRCm38)	P736L	probably benign	Het
Cep290	T	A	10: 100,537,718 (GRCm38)	F1287I	probably damaging	Het
Cntn1	T	C	15: 92,232,275 (GRCm38)		probably null	Het
Col6a3	C	T	1: 90,822,291 (GRCm38)	G274R	probably damaging	Het
Cplane1	G	T	15: 8,180,915 (GRCm38)	V291F	probably damaging	Het
Cyb5r4	T	C	9: 87,055,782 (GRCm38)	C285R	probably damaging	Het
Cyp4f39	G	A	17: 32,489,655 (GRCm38)	C392Y	probably damaging	Het
Dcun1d3	A	T	7: 119,859,511 (GRCm38)	D100E	probably damaging	Het
Dhx58	A	T	11: 100,698,171 (GRCm38)	D516E	probably benign	Het
Dock5	T	A	14: 67,828,502 (GRCm38)	I351F	probably benign	Het
Elmod2	A	C	8: 83,319,412 (GRCm38)		probably null	Het
Endov	G	A	11: 119,507,251 (GRCm38)	A281T	probably benign	Het
Epyc	A	G	10: 97,649,700 (GRCm38)	M1V	probably null	Het
Espnl	T	A	1: 91,323,568 (GRCm38)	H128Q	probably damaging	Het
Fam20a	A	T	11: 109,674,628 (GRCm38)	C452*	probably null	Het
Fam241b	A	G	10: 62,108,954 (GRCm38)	V88A	probably damaging	Het
Fbxl9	A	G	8: 105,315,667 (GRCm38)		probably benign	Het
Fgd3	A	T	13: 49,296,690 (GRCm38)	S28T	possibly damaging	Het
Fmn1	C	A	2: 113,525,680 (GRCm38)	P920Q	unknown	Het
Gpr139	G	C	7: 119,144,866 (GRCm38)	D165E	probably benign	Het
Hoxb1	A	G	11: 96,367,101 (GRCm38)	T286A	possibly damaging	Het
Ifi204	T	A	1: 173,759,568 (GRCm38)	E174D	probably benign	Het
Igf2bp2	A	G	16: 22,061,882 (GRCm38)	I555T	possibly damaging	Het
Ighv1-85	A	G	12: 116,000,179 (GRCm38)	I67T	probably damaging	Het
Ihh	G	C	1: 74,951,147 (GRCm38)	P23R	unknown	Het
Irx2	T	C	13: 72,631,277 (GRCm38)	S227P	probably damaging	Het
Itga4	A	G	2: 79,256,182 (GRCm38)	I68V	probably benign	Het
Jsrp1	T	A	10: 80,812,072 (GRCm38)	T51S	probably benign	Het
Khdc4	T	C	3: 88,711,695 (GRCm38)	S569P	probably damaging	Het
Kifc2	G	T	15: 76,662,810 (GRCm38)	G306V	probably damaging	Het
L3mbtl2	T	A	15: 81,667,387 (GRCm38)	S85T	possibly damaging	Het
Lama1	T	C	17: 67,767,385 (GRCm38)	S944P		Het
Lama4	T	A	10: 39,026,635 (GRCm38)	C202S	probably damaging	Het
Morc3	G	A	16: 93,849,173 (GRCm38)	D218N	probably damaging	Het
Mrtfb	T	A	16: 13,405,854 (GRCm38)	Y866*	probably null	Het
Myorg	A	G	4: 41,498,577 (GRCm38)	I351T	probably damaging	Het
N4bp2l1	G	A	5: 150,572,924 (GRCm38)	T179I	probably damaging	Het
Narf	A	G	11: 121,249,150 (GRCm38)	E270G	probably benign	Het
Nsd2	A	G	5: 33,892,036 (GRCm38)	D1205G	probably damaging	Het
Or10x1	T	C	1: 174,369,193 (GRCm38)	V92A	probably benign	Het
Or5an11	T	C	19: 12,268,704 (GRCm38)	V158A	probably benign	Het
Parl	T	C	16: 20,287,875 (GRCm38)	T195A	probably benign	Het
Phrf1	A	G	7: 141,240,933 (GRCm38)	I158V	unknown	Het
Phtf1	T	C	3: 103,997,664 (GRCm38)	F543L	possibly damaging	Het
Polr1a	G	T	6: 71,950,879 (GRCm38)	K871N	possibly damaging	Het
Ppp2r5a	A	T	1: 191,357,801 (GRCm38)	I252K	probably damaging	Het
Ptgir	T	A	7: 16,907,048 (GRCm38)	D88E	probably damaging	Het
Raly	T	C	2: 154,857,420 (GRCm38)	V48A	probably damaging	Het
Ripor1	T	A	8: 105,617,815 (GRCm38)	L527*	probably null	Het
Rnf213	T	C	11: 119,416,547 (GRCm38)	S678P		Het
Rpf1	T	A	3: 146,507,163 (GRCm38)	Q306L	probably benign	Het
Rpl14	T	C	9: 120,574,105 (GRCm38)	I122T	probably damaging	Het
Scn9a	C	A	2: 66,484,404 (GRCm38)	A1657S	possibly damaging	Het
Serpinb10	A	G	1: 107,546,747 (GRCm38)	Y213C	probably damaging	Het
Slc25a23	A	G	17: 57,052,827 (GRCm38)	L308P	probably damaging	Het
Smg9	T	A	7: 24,420,633 (GRCm38)	M387K	probably benign	Het
Socs3	G	A	11: 117,967,788 (GRCm38)	P148L	probably benign	Het
Susd3	A	G	13: 49,248,430 (GRCm38)	L14P	probably benign	Het
Syt14	T	A	1: 192,980,550 (GRCm38)	M80L	probably benign	Het
Tmprss2	T	A	16: 97,568,416 (GRCm38)	Y386F	possibly damaging	Het
Tmx3	T	A	18: 90,540,071 (GRCm38)	S416T	probably benign	Het
Treh	A	G	9: 44,685,948 (GRCm38)	T555A	probably benign	Het
Ttc5	T	G	14: 50,765,943 (GRCm38)	Q428P	probably damaging	Het
Vmn2r73	A	G	7: 85,871,984 (GRCm38)	S259P	possibly damaging	Het
Vps4b	A	T	1: 106,791,704 (GRCm38)	V38E	probably damaging	Het
Wdr83	C	A	8: 85,076,261 (GRCm38)	R177L	probably benign	Het
Zfp780b	A	G	7: 27,963,163 (GRCm38)	F656L	possibly damaging	Het
Zfp995	A	T	17: 21,880,660 (GRCm38)	F198I	probably benign	Het
Zswim8	A	T	14: 20,721,484 (GRCm38)	Y1495F	probably damaging	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
R0270:Plod2	UTSW	9	92,584,521 (GRCm38)	missense	probably benign	0.10
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
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'- GTTAGACCTCATGACTTCCCAGC -3'
(R):5'- CACCACTCCATGCTGGTTAC -3'

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

Posted On

2019-06-26