Mutagenetix > Incidental Mutation

Incidental Mutation 'R0393:Plod1'

31785

Institutional Source

Beutler Lab

Gene Symbol

Plod1

Ensembl Gene

ENSMUSG00000019055

Gene Name

procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1

Synonyms

2410042F05Rik, LH1, lysyl hydroxylase 1

MMRRC Submission

038599-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0393 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

147994210-148021224 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 148003298 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 509 (L509Q)

Ref Sequence

ENSEMBL: ENSMUSP00000019199 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000019199]

AlphaFold

Q9R0E2

Predicted Effect

probably null
Transcript: ENSMUST00000019199
AA Change: L509Q

PolyPhen 2 Score 0.350 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000019199
Gene: ENSMUSG00000019055
AA Change: L509Q

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
low complexity region	301	313	N/A	INTRINSIC
Blast:P4Hc	444	492	1e-8	BLAST
P4Hc	554	727	4.87e-26	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124041

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124292

Predicted Effect

probably null
Transcript: ENSMUST00000149129
AA Change: L95Q

SMART Domains

Protein: ENSMUSP00000118857
Gene: ENSMUSG00000019055
AA Change: L95Q

Domain	Start	End	E-Value	Type
Blast:P4Hc	31	136	5e-33	BLAST
Blast:P4Hc	141	269	4e-47	BLAST

Meta Mutation Damage Score

0.4857

Coding Region Coverage

1x: 99.2%
3x: 98.3%
10x: 96.3%
20x: 92.9%

Validation Efficiency

100% (59/59)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the 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 VI have deficiencies in lysyl hydroxylase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
PHENOTYPE: Mice homozygous for a null allele exhibit hypotonia, reduced voluntary movement, abnormal aorta and skin collagen fibers, irregular vascular smooth muscle and premature death associated with thoracic cavity hemorrhage and aortic dissection. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc9	C	T	6: 142,591,604 (GRCm39)		probably benign	Het
Akr1b7	T	G	6: 34,392,335 (GRCm39)	Y49*	probably null	Het
Ankrd10	G	T	8: 11,685,482 (GRCm39)	R46S	possibly damaging	Het
Atp13a5	A	G	16: 29,085,681 (GRCm39)		probably benign	Het
Baz1a	A	G	12: 54,965,221 (GRCm39)		probably null	Het
Bicd2	C	T	13: 49,533,346 (GRCm39)	T644M	probably damaging	Het
Ccr9	A	T	9: 123,609,035 (GRCm39)	H239L	probably benign	Het
Cd180	A	T	13: 102,842,408 (GRCm39)	N485Y	probably damaging	Het
Ces1d	T	A	8: 93,919,400 (GRCm39)	S131C	probably damaging	Het
Cnpy2	T	A	10: 128,162,076 (GRCm39)	S116R	probably benign	Het
Crym	T	C	7: 119,788,972 (GRCm39)	K285R	probably benign	Het
Cyp2a4	A	T	7: 26,012,293 (GRCm39)	I359F	possibly damaging	Het
Cyp2b10	T	A	7: 25,614,359 (GRCm39)		probably benign	Het
Dcpp3	A	T	17: 24,136,925 (GRCm39)		probably benign	Het
Dnah8	T	A	17: 30,927,364 (GRCm39)	I1340K	probably benign	Het
Fbln1	T	C	15: 85,111,277 (GRCm39)	C144R	probably damaging	Het
Gm1553	T	C	10: 82,328,010 (GRCm39)	R66G	unknown	Het
Il10rb	G	A	16: 91,208,898 (GRCm39)	V103I	probably benign	Het
Irak1bp1	T	A	9: 82,728,614 (GRCm39)	W182R	probably benign	Het
Kcna3	T	C	3: 106,944,315 (GRCm39)	S193P	probably damaging	Het
Kif14	C	T	1: 136,410,156 (GRCm39)	H628Y	probably damaging	Het
Krt31	A	G	11: 99,941,079 (GRCm39)	L77P	probably damaging	Het
Krt36	C	T	11: 99,994,940 (GRCm39)	A211T	possibly damaging	Het
L3mbtl2	C	T	15: 81,552,942 (GRCm39)	A125V	probably damaging	Het
Lmo7	A	G	14: 102,137,892 (GRCm39)	T743A	probably benign	Het
Lyst	C	T	13: 13,821,664 (GRCm39)	T1346M	probably benign	Het
Mapkbp1	T	A	2: 119,843,384 (GRCm39)		probably null	Het
Mif	T	C	10: 75,695,638 (GRCm39)	D55G	probably benign	Het
Mlh3	G	T	12: 85,314,361 (GRCm39)	C608*	probably null	Het
Mlip	A	T	9: 77,146,859 (GRCm39)	C85S	probably benign	Het
Mug1	T	C	6: 121,826,809 (GRCm39)	S211P	possibly damaging	Het
Mybl2	T	A	2: 162,903,528 (GRCm39)		probably benign	Het
Myh8	C	T	11: 67,196,843 (GRCm39)		probably benign	Het
Nanos1	A	G	19: 60,745,368 (GRCm39)	Y222C	probably damaging	Het
Or10ag52	A	T	2: 87,044,037 (GRCm39)	Y267F	probably benign	Het
Or2n1e	G	T	17: 38,585,774 (GRCm39)	M37I	probably benign	Het
Or5d16	T	C	2: 87,773,909 (GRCm39)	D21G	possibly damaging	Het
Papolb	A	G	5: 142,515,211 (GRCm39)	V144A	probably damaging	Het
Pctp	A	G	11: 89,876,945 (GRCm39)	S185P	probably benign	Het
Ppp1r13b	C	A	12: 111,802,122 (GRCm39)	M290I	probably benign	Het
Ralb	G	C	1: 119,405,856 (GRCm39)		probably null	Het
Rxylt1	T	C	10: 121,931,841 (GRCm39)		probably benign	Het
Slc4a8	T	A	15: 100,672,519 (GRCm39)	D18E	probably damaging	Het
Speg	A	C	1: 75,400,568 (GRCm39)	H2576P	possibly damaging	Het
Spock1	T	C	13: 57,588,349 (GRCm39)	D241G	probably damaging	Het
Tcam1	T	A	11: 106,175,040 (GRCm39)	V165E	probably benign	Het
Thbs1	T	A	2: 117,943,472 (GRCm39)	V30E	possibly damaging	Het
Tll2	A	G	19: 41,077,265 (GRCm39)	Y834H	possibly damaging	Het
Trpm6	G	A	19: 18,756,008 (GRCm39)	D84N	probably damaging	Het
Ubr1	T	A	2: 120,737,427 (GRCm39)	Q1039L	probably damaging	Het
Ubr4	A	G	4: 139,138,171 (GRCm39)		probably benign	Het
Vmn1r74	T	C	7: 11,581,242 (GRCm39)	Y181H	possibly damaging	Het
Vmn2r13	T	C	5: 109,304,395 (GRCm39)	T679A	probably benign	Het
Vmn2r91	A	T	17: 18,325,712 (GRCm39)	Y110F	probably damaging	Het
Zbtb40	A	C	4: 136,745,842 (GRCm39)	S64A	probably benign	Het
Zfp184	T	A	13: 22,131,252 (GRCm39)		probably benign	Het

Other mutations in Plod1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01144:Plod1	APN	4	148,017,211 (GRCm39)	missense	probably benign	0.12
IGL02312:Plod1	APN	4	148,010,614 (GRCm39)	missense	probably benign	0.09
IGL02588:Plod1	APN	4	147,997,747 (GRCm39)	nonsense	probably null
IGL02712:Plod1	APN	4	148,003,344 (GRCm39)	missense	possibly damaging	0.95
IGL02976:Plod1	APN	4	147,997,778 (GRCm39)	missense	probably damaging	0.99
IGL03244:Plod1	APN	4	148,007,580 (GRCm39)	critical splice donor site	probably null
R1216:Plod1	UTSW	4	148,005,584 (GRCm39)	missense	probably damaging	0.98
R1897:Plod1	UTSW	4	148,010,657 (GRCm39)	missense	probably damaging	0.97
R3776:Plod1	UTSW	4	148,015,734 (GRCm39)	missense	possibly damaging	0.75
R3923:Plod1	UTSW	4	148,000,280 (GRCm39)	missense	possibly damaging	0.62
R4718:Plod1	UTSW	4	148,000,701 (GRCm39)	intron	probably benign
R4897:Plod1	UTSW	4	148,004,736 (GRCm39)	missense	probably benign
R5173:Plod1	UTSW	4	148,000,758 (GRCm39)	intron	probably benign
R5657:Plod1	UTSW	4	148,003,238 (GRCm39)	missense	possibly damaging	0.46
R6298:Plod1	UTSW	4	148,000,772 (GRCm39)	intron	probably benign
R6995:Plod1	UTSW	4	148,000,675 (GRCm39)	intron	probably benign
R7176:Plod1	UTSW	4	147,997,744 (GRCm39)	missense	probably benign	0.00
R7632:Plod1	UTSW	4	148,011,481 (GRCm39)	missense	probably damaging	1.00
R8059:Plod1	UTSW	4	148,012,941 (GRCm39)	missense	probably damaging	1.00
R8167:Plod1	UTSW	4	148,004,658 (GRCm39)	missense	probably damaging	1.00
R8804:Plod1	UTSW	4	147,997,778 (GRCm39)	missense	probably damaging	0.99
R8909:Plod1	UTSW	4	148,011,563 (GRCm39)	nonsense	probably null
R8986:Plod1	UTSW	4	147,997,734 (GRCm39)	missense	probably damaging	0.99
R9245:Plod1	UTSW	4	148,010,626 (GRCm39)	missense	possibly damaging	0.86
R9646:Plod1	UTSW	4	148,016,112 (GRCm39)	missense	probably benign	0.03
X0013:Plod1	UTSW	4	148,011,499 (GRCm39)	missense	possibly damaging	0.70
Y5406:Plod1	UTSW	4	148,015,644 (GRCm39)	missense	probably damaging	1.00
Y5408:Plod1	UTSW	4	148,015,644 (GRCm39)	missense	probably damaging	1.00
Z1176:Plod1	UTSW	4	148,007,657 (GRCm39)	missense	probably damaging	0.99
Z1177:Plod1	UTSW	4	148,016,178 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- AGCCAGGGAAGACCCATCTTAGAAC -3'
(R):5'- TGGGAGCACATACTGTACTCACAGG -3'

Sequencing Primer
(F):5'- GGGCTCAATTAAGTCATAGCTCC -3'
(R):5'- ACTGTACTCACAGGTCTTTAATCTGG -3'

Posted On

2013-04-24