Mutagenetix > Incidental Mutation

Incidental Mutation 'R8062:Plod3'

619773

Institutional Source

Beutler Lab

Gene Symbol

Plod3

Ensembl Gene

ENSMUSG00000004846

Gene Name

procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3

Synonyms

LH3, lysyl hydroxylase 3

MMRRC Submission

067498-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8062 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

137015873-137025500 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 137019123 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 336 (H336L)

Ref Sequence

ENSEMBL: ENSMUSP00000004968 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000004968] [ENSMUST00000034953] [ENSMUST00000085941] [ENSMUST00000111090] [ENSMUST00000111091] [ENSMUST00000137272] [ENSMUST00000156963]

AlphaFold

Q9R0E1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000004968
AA Change: H336L

PolyPhen 2 Score 0.872 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: H336L

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
low complexity region	312	324	N/A	INTRINSIC
Blast:P4Hc	456	502	2e-8	BLAST
P4Hc	567	740	1.43e-23	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000034953

SMART Domains

Protein: ENSMUSP00000034953
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	14	26	N/A	INTRINSIC
low complexity region	58	73	N/A	INTRINSIC
Pfam:zf-HIT	112	141	6.3e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000085941

SMART Domains

Protein: ENSMUSP00000083103
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	15	27	N/A	INTRINSIC
low complexity region	59	74	N/A	INTRINSIC
Pfam:zf-HIT	113	142	3e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000111090

SMART Domains

Protein: ENSMUSP00000106719
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	14	26	N/A	INTRINSIC
low complexity region	58	73	N/A	INTRINSIC
Pfam:zf-HIT	112	141	2.2e-14	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000111091

SMART Domains

Protein: ENSMUSP00000106720
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	19	31	N/A	INTRINSIC
low complexity region	63	78	N/A	INTRINSIC
Pfam:zf-HIT	117	146	2.1e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000127100

SMART Domains

Protein: ENSMUSP00000123550
Gene: ENSMUSG00000004846

Domain	Start	End	E-Value	Type
Blast:P4Hc	2	35	2e-11	BLAST
P4Hc	38	200	3.04e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000137272

SMART Domains

Protein: ENSMUSP00000120331
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	19	31	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000156963

SMART Domains

Protein: ENSMUSP00000115929
Gene: ENSMUSG00000059518

Domain	Start	End	E-Value	Type
low complexity region	14	26	N/A	INTRINSIC
low complexity region	58	73	N/A	INTRINSIC
Pfam:zf-HIT	112	141	6.7e-13	PFAM

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

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. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice display embryonic lethality, reduced embryonic growth, fragility, and fragmented basement membranes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abce1	A	T	8: 80,427,773 (GRCm39)	Y172N	possibly damaging	Het
Abhd2	T	A	7: 78,975,338 (GRCm39)	M176K	possibly damaging	Het
Adamts14	A	G	10: 61,036,140 (GRCm39)		probably null	Het
Atg2a	T	C	19: 6,302,609 (GRCm39)		probably null	Het
Bach2	G	A	4: 32,562,937 (GRCm39)	G468E	probably damaging	Het
Bap1	T	A	14: 30,979,465 (GRCm39)	N489K	probably benign	Het
Btaf1	G	A	19: 36,969,865 (GRCm39)	V1180I	probably benign	Het
Calm5	A	G	13: 3,904,405 (GRCm39)	H33R	probably benign	Het
Cby2	A	T	14: 75,830,046 (GRCm39)	I49N	probably benign	Het
Cnr1	T	A	4: 33,944,707 (GRCm39)	V365E	possibly damaging	Het
Crym	A	C	7: 119,800,391 (GRCm39)	V77G	probably damaging	Het
Cyp2j7	T	A	4: 96,103,587 (GRCm39)	E316V	probably null	Het
Dab2	G	A	15: 6,456,822 (GRCm39)	G233D	probably damaging	Het
Ddx19b	A	T	8: 111,747,611 (GRCm39)	S108T	probably benign	Het
Dsc2	C	T	18: 20,165,331 (GRCm39)	G881R	possibly damaging	Het
Duxf1	G	A	10: 58,059,632 (GRCm39)	A374V	unknown	Het
Duxf3	A	C	10: 58,066,750 (GRCm39)	M93R	probably benign	Het
Duxf3	G	A	10: 58,066,889 (GRCm39)	L537F	probably damaging	Het
Eif2s2	A	G	2: 154,719,724 (GRCm39)	F182L	possibly damaging	Het
Erlin1	T	A	19: 44,044,598 (GRCm39)	K156I	probably benign	Het
Gapvd1	A	G	2: 34,568,126 (GRCm39)	S1413P	probably benign	Het
Gm1110	G	A	9: 26,793,117 (GRCm39)	A553V	probably damaging	Het
Gm3250	C	A	10: 77,618,234 (GRCm39)	C48F	unknown	Het
Gm3604	T	C	13: 62,518,155 (GRCm39)	S68G	probably damaging	Het
Golga5	T	A	12: 102,450,739 (GRCm39)	M464K	probably benign	Het
Gpr142	G	A	11: 114,697,357 (GRCm39)	R301Q	probably benign	Het
Gria4	C	T	9: 4,480,273 (GRCm39)	D392N	possibly damaging	Het
Grik2	T	A	10: 49,116,863 (GRCm39)	T633S	probably damaging	Het
Gsap	T	A	5: 21,399,461 (GRCm39)	I54N	probably damaging	Het
Hdlbp	A	G	1: 93,366,064 (GRCm39)	Y40H	probably benign	Het
Hyal5	C	A	6: 24,876,196 (GRCm39)	T23K	possibly damaging	Het
Iqank1	G	A	15: 75,918,603 (GRCm39)	R508H	probably benign	Het
Itga6	T	A	2: 71,672,087 (GRCm39)	F834L	probably benign	Het
Klf1	T	A	8: 85,629,928 (GRCm39)	L251Q	probably benign	Het
Kndc1	A	G	7: 139,498,760 (GRCm39)	D558G	probably benign	Het
Ktn1	T	A	14: 47,962,429 (GRCm39)		probably null	Het
Lcmt2	A	G	2: 120,970,753 (GRCm39)	V110A	possibly damaging	Het
Lgr4	C	T	2: 109,831,282 (GRCm39)	R304C	probably damaging	Het
Lnpk	T	A	2: 74,381,407 (GRCm39)	I119L	possibly damaging	Het
Med13	A	G	11: 86,210,264 (GRCm39)	V626A	probably benign	Het
Mroh9	A	T	1: 162,866,544 (GRCm39)	L700M	probably damaging	Het
Muc4	T	A	16: 32,577,123 (GRCm39)	W138R		Het
Myh2	G	T	11: 67,084,209 (GRCm39)	E1611*	probably null	Het
Myo9b	T	G	8: 71,774,457 (GRCm39)	S323A	probably damaging	Het
Or2n1c	A	T	17: 38,520,065 (GRCm39)	I310F	probably benign	Het
Or4c52	T	A	2: 89,846,080 (GRCm39)	F269I	possibly damaging	Het
Or5t7	A	C	2: 86,507,410 (GRCm39)	V89G	probably benign	Het
Or8b101	G	T	9: 38,020,213 (GRCm39)	C72F	probably damaging	Het
P2ry13	A	T	3: 59,117,703 (GRCm39)	M25K	probably benign	Het
Pan3	T	A	5: 147,463,960 (GRCm39)	F571Y	probably benign	Het
Pdcd11	A	G	19: 47,119,152 (GRCm39)	D1831G	possibly damaging	Het
Peg10	CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG	CCACATCAGGATCCACATCAGGATGCACATCAG	6: 4,756,398 (GRCm39)		probably benign	Het
Pex1	T	G	5: 3,655,656 (GRCm39)	M161R	probably benign	Het
Piezo2	T	A	18: 63,163,537 (GRCm39)	D2127V	possibly damaging	Het
Pp2d1	A	T	17: 53,822,798 (GRCm39)	N89K	probably benign	Het
Ppp4r3a	A	G	12: 101,008,230 (GRCm39)	S736P	probably damaging	Het
Prp2	C	A	6: 132,577,651 (GRCm39)	Q313K	unknown	Het
Psma5	T	G	3: 108,173,795 (GRCm39)	D90E	probably benign	Het
Reln	G	A	5: 22,176,990 (GRCm39)	T1892I	probably benign	Het
Rictor	C	T	15: 6,801,635 (GRCm39)	S441L	probably benign	Het
Rsf1	T	G	7: 97,326,594 (GRCm39)	D1039E		Het
Rtel1	A	G	2: 180,982,360 (GRCm39)	D370G	probably benign	Het
Scyl2	T	A	10: 89,490,022 (GRCm39)	N447Y	probably damaging	Het
Sis	A	T	3: 72,828,321 (GRCm39)	Y1222*	probably null	Het
Slc37a3	A	T	6: 39,341,530 (GRCm39)	H35Q	probably damaging	Het
Sltm	A	T	9: 70,480,779 (GRCm39)	K210N	unknown	Het
Spata3	T	C	1: 85,952,148 (GRCm39)	I134T	unknown	Het
Speer4d	A	T	5: 15,825,437 (GRCm39)	N54I	possibly damaging	Het
Syne1	A	G	10: 5,135,394 (GRCm39)		probably null	Het
Tars1	A	T	15: 11,388,400 (GRCm39)	F465Y	possibly damaging	Het
Tlr4	T	G	4: 66,758,087 (GRCm39)	N293K	probably benign	Het
Tmprss13	C	A	9: 45,239,986 (GRCm39)	T98K	unknown	Het
Tnfsf8	G	A	4: 63,779,432 (GRCm39)		probably benign	Het
Trim30b	T	A	7: 104,015,393 (GRCm39)		probably benign	Het
Trpm1	A	G	7: 63,851,689 (GRCm39)	K136E	probably benign	Het
Ttc6	A	G	12: 57,783,764 (GRCm39)	Y1741C	possibly damaging	Het
Usp38	T	C	8: 81,711,218 (GRCm39)	D939G	probably damaging	Het
Vmn1r196	T	A	13: 22,477,440 (GRCm39)	N26K	probably damaging	Het
Vmn2r50	C	A	7: 9,774,240 (GRCm39)		probably null	Het
Wdr3	T	A	3: 100,049,810 (GRCm39)	M773L	probably benign	Het
Zfp993	T	G	4: 146,739,415 (GRCm39)		probably null	Het

Other mutations in Plod3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00507:Plod3	APN	5	137,025,030 (GRCm39)	missense	possibly damaging	0.78
IGL01090:Plod3	APN	5	137,019,090 (GRCm39)	missense	probably benign	0.37
IGL01443:Plod3	APN	5	137,019,075 (GRCm39)	missense	probably benign	0.17
IGL01583:Plod3	APN	5	137,025,002 (GRCm39)	missense	probably benign	0.02
R0544:Plod3	UTSW	5	137,020,465 (GRCm39)	missense	probably benign	0.09
R0747:Plod3	UTSW	5	137,017,049 (GRCm39)	missense	probably benign	0.34
R0764:Plod3	UTSW	5	137,018,437 (GRCm39)	unclassified	probably benign
R1520:Plod3	UTSW	5	137,020,165 (GRCm39)	missense	probably damaging	0.99
R1631:Plod3	UTSW	5	137,017,847 (GRCm39)	missense	probably damaging	1.00
R1751:Plod3	UTSW	5	137,019,030 (GRCm39)	missense	possibly damaging	0.89
R1767:Plod3	UTSW	5	137,019,030 (GRCm39)	missense	possibly damaging	0.89
R1984:Plod3	UTSW	5	137,019,707 (GRCm39)	splice site	probably null
R1985:Plod3	UTSW	5	137,019,707 (GRCm39)	splice site	probably null
R2137:Plod3	UTSW	5	137,017,571 (GRCm39)	missense	probably damaging	1.00
R2148:Plod3	UTSW	5	137,016,627 (GRCm39)	nonsense	probably null
R2179:Plod3	UTSW	5	137,019,862 (GRCm39)	missense	possibly damaging	0.77
R2318:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2319:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2512:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2513:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2696:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2891:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R2893:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R3030:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R3439:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R3957:Plod3	UTSW	5	137,023,046 (GRCm39)	missense	probably damaging	1.00
R4080:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4081:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4342:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4344:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4345:Plod3	UTSW	5	137,017,000 (GRCm39)	missense	probably benign	0.38
R4546:Plod3	UTSW	5	137,017,801 (GRCm39)	missense	possibly damaging	0.94
R4799:Plod3	UTSW	5	137,019,654 (GRCm39)	missense	probably benign	0.00
R4843:Plod3	UTSW	5	137,019,854 (GRCm39)	nonsense	probably null
R4956:Plod3	UTSW	5	137,018,772 (GRCm39)	missense	probably damaging	1.00
R5159:Plod3	UTSW	5	137,023,932 (GRCm39)	intron	probably benign
R5162:Plod3	UTSW	5	137,020,161 (GRCm39)	missense	probably damaging	1.00
R5328:Plod3	UTSW	5	137,018,537 (GRCm39)	missense	probably damaging	1.00
R5427:Plod3	UTSW	5	137,020,642 (GRCm39)	missense	probably damaging	1.00
R6627:Plod3	UTSW	5	137,017,310 (GRCm39)	missense	probably damaging	0.99
R7003:Plod3	UTSW	5	137,018,498 (GRCm39)	missense	probably damaging	1.00
R7132:Plod3	UTSW	5	137,023,971 (GRCm39)	missense
R7376:Plod3	UTSW	5	137,019,335 (GRCm39)	missense	probably benign	0.00
R7404:Plod3	UTSW	5	137,023,901 (GRCm39)	missense	probably benign
R7827:Plod3	UTSW	5	137,018,835 (GRCm39)	missense	probably benign
R8506:Plod3	UTSW	5	137,017,830 (GRCm39)	missense	probably damaging	1.00
R8772:Plod3	UTSW	5	137,017,773 (GRCm39)	missense	probably damaging	0.99
R9108:Plod3	UTSW	5	137,018,017 (GRCm39)	missense	probably damaging	0.99
R9439:Plod3	UTSW	5	137,023,036 (GRCm39)	missense	probably benign	0.03
R9788:Plod3	UTSW	5	137,019,911 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GAGGCTGTGGATTCTGCAAC -3'
(R):5'- CTGCAATATGAGGCTCGTGG -3'

Sequencing Primer
(F):5'- ACAGCACGGATGTCAGC -3'
(R):5'- TGGTACACCTCCTGAAGATGG -3'

Posted On

2020-01-23