Mutagenetix > Incidental Mutation

Incidental Mutation 'R9646:Plod1'

726717

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9646 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

147994210-148021224 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 148016112 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Lysine at position 93 (E93K)

Ref Sequence

ENSEMBL: ENSMUSP00000019199 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000019199] [ENSMUST00000105712]

AlphaFold

Q9R0E2

Predicted Effect

probably benign
Transcript: ENSMUST00000019199
AA Change: E93K

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000019199
Gene: ENSMUSG00000019055
AA Change: E93K

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

probably benign
Transcript: ENSMUST00000105712
AA Change: E93K

PolyPhen 2 Score 0.408 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000101337
Gene: ENSMUSG00000019055
AA Change: E93K

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrl2	A	T	3: 148,544,926 (GRCm39)	I723N	probably damaging	Het
Agbl1	G	A	7: 76,075,648 (GRCm39)	R682Q	unknown	Het
Ankrd42	A	T	7: 92,273,257 (GRCm39)	D123E	possibly damaging	Het
Anxa4	A	T	6: 86,730,814 (GRCm39)	I121N	probably damaging	Het
Asic1	T	C	15: 99,593,414 (GRCm39)	F257S	probably benign	Het
Catsper2	TAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCT	TAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCT	2: 121,228,053 (GRCm39)		probably benign	Het
Cckar	T	C	5: 53,863,608 (GRCm39)	T118A	probably benign	Het
Cfap61	T	A	2: 145,854,152 (GRCm39)	I388N	probably damaging	Het
Chrnd	A	T	1: 87,120,311 (GRCm39)	I156F	probably damaging	Het
Col15a1	T	A	4: 47,257,187 (GRCm39)	L326Q	possibly damaging	Het
Dcpp3	A	T	17: 24,138,156 (GRCm39)	I105L	possibly damaging	Het
Dnaaf5	T	A	5: 139,151,832 (GRCm39)	H494Q	probably benign	Het
Dph5	T	A	3: 115,708,692 (GRCm39)	Y125N	probably damaging	Het
Eif4enif1	T	C	11: 3,170,280 (GRCm39)	V111A	probably damaging	Het
Etl4	T	A	2: 20,802,724 (GRCm39)	I1010K	probably benign	Het
Faf1	T	A	4: 109,652,016 (GRCm39)	W236R	probably damaging	Het
Fat4	A	G	3: 39,035,813 (GRCm39)	D3155G	probably damaging	Het
Fhip2b	T	C	14: 70,827,808 (GRCm39)	H125R	probably damaging	Het
Firrm	A	G	1: 163,822,195 (GRCm39)	V32A	probably damaging	Het
Galnt12	T	C	4: 47,120,390 (GRCm39)	I491T	probably damaging	Het
Gm10553	T	A	1: 85,077,901 (GRCm39)	L6Q	probably damaging	Het
H2-T10	A	T	17: 36,431,157 (GRCm39)	I168N	probably damaging	Het
Hdac9	T	A	12: 34,487,167 (GRCm39)	Q78L	probably damaging	Het
Hmx1	C	T	5: 35,549,400 (GRCm39)	T231M	probably damaging	Het
Hrob	A	T	11: 102,146,586 (GRCm39)	Q287H	possibly damaging	Het
Hsd17b13	T	C	5: 104,124,973 (GRCm39)	K70R	probably null	Het
Hykk	C	T	9: 54,853,521 (GRCm39)	T281I	probably benign	Het
Il1r2	A	G	1: 40,162,362 (GRCm39)	D335G	probably damaging	Het
Insig2	A	C	1: 121,240,040 (GRCm39)	L87V	probably damaging	Het
Insrr	A	T	3: 87,721,805 (GRCm39)	Y1193F	probably damaging	Het
Itpr1	A	G	6: 108,371,845 (GRCm39)	Y1173C	probably damaging	Het
Kcnh8	A	G	17: 53,104,573 (GRCm39)	N190S	probably benign	Het
Kntc1	T	C	5: 123,897,119 (GRCm39)	F161L	probably benign	Het
Lilra5	T	C	7: 4,244,907 (GRCm39)	L226P	probably damaging	Het
Muc2	C	T	7: 141,276,643 (GRCm39)	A11V	probably benign	Het
Nrp2	T	C	1: 62,777,566 (GRCm39)	F124L	probably damaging	Het
Or52e4	T	C	7: 104,706,374 (GRCm39)	I307T	probably benign	Het
Or5m11b	T	A	2: 85,806,446 (GRCm39)	N286K	probably benign	Het
Or5w15	T	A	2: 87,568,512 (GRCm39)	D52V	probably damaging	Het
Or8c19-ps1	T	A	9: 38,220,114 (GRCm39)	S8T	probably damaging	Het
Pcdhb17	A	T	18: 37,618,471 (GRCm39)	N87I	possibly damaging	Het
Pdgfrb	T	A	18: 61,211,721 (GRCm39)		probably null	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Pepd	A	T	7: 34,620,882 (GRCm39)	Q49L	possibly damaging	Het
Pigo	C	A	4: 43,017,967 (GRCm39)	R1083L	probably damaging	Het
Pitpnm1	G	A	19: 4,153,269 (GRCm39)	D142N	probably damaging	Het
Pramel11	A	T	4: 143,623,634 (GRCm39)	V180E	probably damaging	Het
Rev3l	T	C	10: 39,698,440 (GRCm39)	I979T	probably damaging	Het
Scrib	C	T	15: 75,932,492 (GRCm39)	G743D	probably damaging	Het
Septin3	T	C	15: 82,170,088 (GRCm39)	S205P	probably benign	Het
Sez6	A	G	11: 77,867,632 (GRCm39)	K850E	probably damaging	Het
Sfxn5	T	A	6: 85,266,195 (GRCm39)	T101S	probably damaging	Het
Slc6a5	A	T	7: 49,567,496 (GRCm39)	K317*	probably null	Het
Sox8	A	T	17: 25,786,871 (GRCm39)	D277E	probably benign	Het
Sptbn2	G	T	19: 4,795,341 (GRCm39)	A1600S	probably damaging	Het
Syne1	A	G	10: 5,179,187 (GRCm39)	V4429A	possibly damaging	Het
Tnrc6b	T	A	15: 80,773,266 (GRCm39)	F1137L	possibly damaging	Het
Trim43a	A	G	9: 88,466,392 (GRCm39)	R238G	probably benign	Het
Triobp	T	C	15: 78,887,934 (GRCm39)	L1943P	probably damaging	Het
Vmn1r125	T	C	7: 21,006,261 (GRCm39)	V53A	possibly damaging	Het
Vwa5b1	T	A	4: 138,319,420 (GRCm39)	N412I	probably damaging	Het
Yipf7	T	A	5: 69,678,424 (GRCm39)	T122S	probably benign	Het
Zfp1005	C	T	2: 150,110,104 (GRCm39)	H265Y	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
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
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
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'- AACTAGCTCATCCGTCATCTCTGG -3'
(R):5'- CCCCTGCGTTGAGTTGAAAG -3'

Sequencing Primer
(F):5'- TCTGGCAGCTTATACCTCACCAAG -3'
(R):5'- CCTGCGTTGAGTTGAAAGGAAGC -3'

Posted On

2022-10-06