Mutagenetix > Incidental Mutation

Incidental Mutation 'R3923:Plod1'

307028

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

040820-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3923 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

147994210-148021224 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 148000280 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamic Acid at position 260 (K260E)

Gene Model

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

AlphaFold

Q9R0E2

Predicted Effect

probably benign
Transcript: ENSMUST00000019199
AA Change: K627E

PolyPhen 2 Score 0.146 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000019199
Gene: ENSMUSG00000019055
AA Change: K627E

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

possibly damaging
Transcript: ENSMUST00000149129
AA Change: K260E

PolyPhen 2 Score 0.619 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000118857
Gene: ENSMUSG00000019055
AA Change: K260E

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

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.1%
20x: 94.3%

Validation Efficiency

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam22	T	C	5: 8,180,514 (GRCm39)	M528V	possibly damaging	Het
Ano3	T	A	2: 110,601,304 (GRCm39)	Y318F	probably damaging	Het
Asic4	T	A	1: 75,427,871 (GRCm39)	D132E	probably damaging	Het
Atp2b2	A	G	6: 113,774,069 (GRCm39)		probably null	Het
Cast	T	C	13: 74,876,532 (GRCm39)	E447G	probably damaging	Het
Ccdc110	T	C	8: 46,395,426 (GRCm39)	I439T	probably damaging	Het
Ccdc50	A	T	16: 27,263,294 (GRCm39)	R264S	probably damaging	Het
Cdhr18	T	A	14: 13,865,990 (GRCm38)	K300*	probably null	Het
Chd9	T	A	8: 91,660,147 (GRCm39)	V369E	probably benign	Het
Cnnm1	A	G	19: 43,428,884 (GRCm39)	M1V	probably null	Het
Col4a1	T	A	8: 11,251,665 (GRCm39)		probably benign	Het
Crtac1	A	G	19: 42,322,386 (GRCm39)	V118A	probably damaging	Het
Ddx59	T	A	1: 136,344,482 (GRCm39)	V51D	probably benign	Het
Dipk1c	A	T	18: 84,748,812 (GRCm39)	T137S	probably damaging	Het
Dtd2	G	C	12: 52,051,734 (GRCm39)		probably null	Het
Ehmt1	A	T	2: 24,774,347 (GRCm39)		probably null	Het
Emc1	T	A	4: 139,090,496 (GRCm39)	L412*	probably null	Het
Ep400	T	C	5: 110,904,389 (GRCm39)	N70S	possibly damaging	Het
Ercc6l2	T	C	13: 64,018,549 (GRCm39)		probably benign	Het
Fry	T	C	5: 150,336,814 (GRCm39)	V1395A	probably benign	Het
Gps1	A	G	11: 120,677,259 (GRCm39)	N186S	possibly damaging	Het
Hdgf	T	A	3: 87,821,535 (GRCm39)	D128E	probably benign	Het
Hipk3	A	G	2: 104,301,107 (GRCm39)	S362P	probably damaging	Het
Hypk	C	A	2: 121,288,683 (GRCm39)	H116Q	possibly damaging	Het
Ifna9	T	A	4: 88,510,508 (GRCm39)	T39S	possibly damaging	Het
Itgae	A	C	11: 73,006,969 (GRCm39)	D405A	probably damaging	Het
Itprid1	T	C	6: 55,945,045 (GRCm39)	S589P	probably benign	Het
Kdm5a	T	C	6: 120,358,625 (GRCm39)	S223P	probably benign	Het
Kif21a	C	T	15: 90,821,497 (GRCm39)	S1432N	possibly damaging	Het
Klhl1	A	T	14: 96,584,316 (GRCm39)	C305S	possibly damaging	Het
Lrrn2	A	G	1: 132,866,230 (GRCm39)	S432G	probably benign	Het
Mlana	T	A	19: 29,682,098 (GRCm39)	S50R	probably damaging	Het
Mycbp2	A	T	14: 103,364,149 (GRCm39)	H4383Q	probably damaging	Het
Ncor1	A	G	11: 62,216,442 (GRCm39)	S1469P	probably damaging	Het
Nol6	G	T	4: 41,121,531 (GRCm39)	F270L	probably benign	Het
Nr2c2	T	A	6: 92,137,382 (GRCm39)	M431K	probably damaging	Het
Nrap	T	C	19: 56,368,688 (GRCm39)	I243V	probably damaging	Het
Obscn	T	C	11: 58,951,754 (GRCm39)	I4297V	possibly damaging	Het
Onecut2	A	G	18: 64,474,591 (GRCm39)	K381E	probably damaging	Het
Or52n1	T	A	7: 104,383,396 (GRCm39)	E58D	probably benign	Het
Or8k23	T	C	2: 86,186,205 (GRCm39)	I174V	probably benign	Het
Palb2	A	T	7: 121,716,583 (GRCm39)		probably null	Het
Rgsl1	T	C	1: 153,679,876 (GRCm39)		probably null	Het
Rpe65	T	A	3: 159,310,037 (GRCm39)	F103L	probably benign	Het
Ryr3	C	T	2: 112,672,218 (GRCm39)	A1438T	possibly damaging	Het
Slc17a3	G	A	13: 24,042,037 (GRCm39)	V402M	possibly damaging	Het
Slc19a3	A	T	1: 83,000,678 (GRCm39)	F113Y	probably damaging	Het
Snph	C	T	2: 151,435,431 (GRCm39)	C430Y	probably damaging	Het
Tarbp1	T	C	8: 127,167,510 (GRCm39)	I1101V	probably benign	Het
Tatdn1	G	A	15: 58,793,020 (GRCm39)	L120F	possibly damaging	Het
Trav3-3	A	G	14: 53,903,828 (GRCm39)	K49E	probably benign	Het
Trpv5	T	C	6: 41,630,183 (GRCm39)	T636A	probably benign	Het
Ube2l6	A	G	2: 84,639,418 (GRCm39)	D127G	possibly damaging	Het
Usp33	T	A	3: 152,080,428 (GRCm39)		probably null	Het
Usp53	A	T	3: 122,727,954 (GRCm39)	F876Y	probably benign	Het
Utrn	A	T	10: 12,615,223 (GRCm39)	I316K	probably benign	Het
Zfp106	G	T	2: 120,365,337 (GRCm39)	Q357K	probably damaging	Het
Zfp143	T	C	7: 109,673,398 (GRCm39)	V138A	probably damaging	Het
Zfp451	T	C	1: 33,818,126 (GRCm39)	R118G	probably null	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
R0393:Plod1	UTSW	4	148,003,298 (GRCm39)	missense	probably null	0.35
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
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'- GTAAAATGACTGTCTAGACGTGC -3'
(R):5'- GGAGTCTGGGTGCCATCTTA -3'

Sequencing Primer
(F):5'- GTGCAAGGCCCTATGTACAATTC -3'
(R):5'- AGTCTGGGTGCCATCTTAGATTCTC -3'

Posted On

2015-04-17