Mutagenetix > Incidental Mutation

Incidental Mutation 'R5328:Plod3'

422130

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

042843-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5328 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

137015873-137025500 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 137018537 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 258 (N258K)

Ref Sequence

ENSEMBL: ENSMUSP00000004968 (fasta)

Gene Model

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

AlphaFold

Q9R0E1

Predicted Effect

probably damaging
Transcript: ENSMUST00000004968
AA Change: N258K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: N258K

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

noncoding transcript
Transcript: ENSMUST00000102285

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

noncoding transcript
Transcript: ENSMUST00000144784

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129896

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137419

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151642

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: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.5%

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1b	T	A	5: 8,887,694 (GRCm39)	V860E	possibly damaging	Het
Abcc6	T	C	7: 45,641,735 (GRCm39)	D881G	probably benign	Het
Abcc9	A	G	6: 142,627,785 (GRCm39)	V415A	probably benign	Het
Adgrb3	A	C	1: 25,133,356 (GRCm39)	N1003K	possibly damaging	Het
Adora3	C	T	3: 105,814,619 (GRCm39)	T123I	probably benign	Het
Amotl2	A	C	9: 102,600,967 (GRCm39)	T345P	probably benign	Het
Arap3	C	T	18: 38,124,740 (GRCm39)	E247K	possibly damaging	Het
Atp8b1	A	T	18: 64,664,462 (GRCm39)	D1235E	probably benign	Het
Axl	A	T	7: 25,472,836 (GRCm39)	V400E	probably damaging	Het
Brd8	T	A	18: 34,741,034 (GRCm39)	N431Y	probably benign	Het
Cadps	A	T	14: 12,457,790 (GRCm38)	N1025K	probably benign	Het
Cblc	A	T	7: 19,526,505 (GRCm39)	S195T	possibly damaging	Het
Chd2	C	T	7: 73,113,429 (GRCm39)	A1184T	possibly damaging	Het
Chst10	G	A	1: 38,935,043 (GRCm39)		probably benign	Het
Col12a1	T	C	9: 79,527,342 (GRCm39)	K2663E	probably damaging	Het
Cspg4	A	T	9: 56,793,140 (GRCm39)	I292L	probably benign	Het
Cul1	T	C	6: 47,485,251 (GRCm39)	V294A	probably damaging	Het
Cyp2d11	G	A	15: 82,275,972 (GRCm39)	P203L	probably benign	Het
Dnaaf10	C	A	11: 17,172,220 (GRCm39)	P103Q	probably damaging	Het
Dscam	T	C	16: 96,474,878 (GRCm39)	H1228R	probably benign	Het
Eif3l	A	T	15: 78,977,561 (GRCm39)	K534*	probably null	Het
Enpep	T	C	3: 129,074,159 (GRCm39)	E796G	probably benign	Het
Ext1	C	A	15: 52,939,213 (GRCm39)	W612L	probably damaging	Het
Faap100	T	A	11: 120,268,458 (GRCm39)	E105V	possibly damaging	Het
Fam117a	T	A	11: 95,254,996 (GRCm39)		probably null	Het
Fan1	A	T	7: 64,004,217 (GRCm39)	Y750N	probably damaging	Het
Fat4	T	A	3: 39,011,017 (GRCm39)	I2039N	probably damaging	Het
Gabrr2	G	T	4: 33,082,565 (GRCm39)	D106Y	probably damaging	Het
Gak	A	C	5: 108,764,867 (GRCm39)	C145G	possibly damaging	Het
Galnt14	A	T	17: 73,812,454 (GRCm39)	N406K	possibly damaging	Het
Gm10439	T	G	X: 148,419,159 (GRCm39)	*434E	probably null	Het
Gm10837	G	T	14: 122,728,190 (GRCm39)	R22L	unknown	Het
Gm19965	T	A	1: 116,749,148 (GRCm39)	H276Q	possibly damaging	Het
Gm43517	T	C	12: 49,437,939 (GRCm39)		probably benign	Het
Greb1l	A	T	18: 10,553,720 (GRCm39)	I1574F	probably damaging	Het
Gzme	G	A	14: 56,355,224 (GRCm39)	H236Y	probably benign	Het
Heatr5b	G	A	17: 79,133,791 (GRCm39)	T266I	possibly damaging	Het
Hk3	T	C	13: 55,161,306 (GRCm39)	I185V	probably benign	Het
Hnrnpr	A	G	4: 136,066,527 (GRCm39)	E302G	probably benign	Het
Itgal	T	C	7: 126,910,847 (GRCm39)		probably null	Het
Itk	A	G	11: 46,222,703 (GRCm39)	S583P	probably benign	Het
Loxhd1	A	T	18: 77,498,268 (GRCm39)	I1448F	probably damaging	Het
Macf1	GCCCCC	GCCCCCC	4: 123,244,784 (GRCm39)		probably null	Het
Man2a2	A	T	7: 80,018,504 (GRCm39)	F118L	probably benign	Het
Mfsd5	T	A	15: 102,189,447 (GRCm39)	V273E	probably damaging	Het
Nfe2l2	A	G	2: 75,507,200 (GRCm39)	L300P	probably damaging	Het
Nt5c1a	T	G	4: 123,102,786 (GRCm39)	L122R	possibly damaging	Het
Nt5c3b	A	G	11: 100,331,067 (GRCm39)	F42S	probably damaging	Het
Or2av9	C	A	11: 58,381,255 (GRCm39)	A109S	possibly damaging	Het
Or51g2	T	A	7: 102,623,175 (GRCm39)	N8I	possibly damaging	Het
Pabpc1	A	T	15: 36,603,121 (GRCm39)	D204E	probably benign	Het
Panx2	A	G	15: 88,952,298 (GRCm39)	N255S	probably damaging	Het
Pcnt	A	G	10: 76,247,553 (GRCm39)	L993P	probably damaging	Het
Pfas	A	T	11: 68,879,418 (GRCm39)	C1160S	probably damaging	Het
Plekhh3	T	A	11: 101,058,484 (GRCm39)		probably benign	Het
Prr14l	T	C	5: 32,987,365 (GRCm39)	Q710R	probably benign	Het
Rnf216	G	T	5: 143,078,754 (GRCm39)	T65K	possibly damaging	Het
Samd9l	T	C	6: 3,376,739 (GRCm39)	E174G	probably damaging	Het
Septin12	T	A	16: 4,811,857 (GRCm39)	M63L	possibly damaging	Het
Sh3bgrl2	T	A	9: 83,459,509 (GRCm39)	D22E	probably benign	Het
Sirpd	T	C	3: 15,397,234 (GRCm39)	M17V	unknown	Het
Skil	A	G	3: 31,171,718 (GRCm39)	K488R	probably benign	Het
Slamf6	T	A	1: 171,765,662 (GRCm39)	I262K	probably benign	Het
Slc27a3	T	C	3: 90,294,139 (GRCm39)	D470G	probably damaging	Het
Sorbs3	A	T	14: 70,418,623 (GRCm39)	V680E	probably damaging	Het
Sox9	C	T	11: 112,673,484 (GRCm39)	T25I	probably benign	Het
Srsf1	G	T	11: 87,940,819 (GRCm39)		probably benign	Het
Stard9	A	C	2: 120,529,711 (GRCm39)	E1989D	probably damaging	Het
Thumpd2	T	A	17: 81,351,591 (GRCm39)	I277F	possibly damaging	Het
Tinag	C	A	9: 76,912,913 (GRCm39)	G299*	probably null	Het
Tk2	A	T	8: 104,955,931 (GRCm39)		probably null	Het
Tmem44	A	G	16: 30,359,709 (GRCm39)	S210P	possibly damaging	Het
Traf3ip1	C	A	1: 91,447,791 (GRCm39)	P423T	probably damaging	Het
Trmt12	A	G	15: 58,744,704 (GRCm39)	D34G	probably damaging	Het
Ttc39b	A	G	4: 83,180,178 (GRCm39)	Y72H	probably damaging	Het
Ttn	G	A	2: 76,708,755 (GRCm39)		probably benign	Het
Ttyh2	T	A	11: 114,600,894 (GRCm39)	I381N	possibly damaging	Het
Uaca	A	T	9: 60,777,814 (GRCm39)	N734Y	probably benign	Het
Usp34	T	C	11: 23,414,616 (GRCm39)	I2853T	probably benign	Het
Usp34	G	A	11: 23,438,659 (GRCm39)	G3407D	probably benign	Het
Vmn2r78	A	G	7: 86,570,238 (GRCm39)	Y252C	probably damaging	Het
Wdr19	G	A	5: 65,401,522 (GRCm39)	C979Y	probably damaging	Het
Yeats2	A	T	16: 19,989,955 (GRCm39)	H277L	probably damaging	Het
Zbtb2	T	C	10: 4,319,267 (GRCm39)	Y253C	possibly damaging	Het
Zfat	C	A	15: 68,051,677 (GRCm39)	G706C	probably damaging	Het
Zfp106	A	T	2: 120,350,898 (GRCm39)	N1584K	possibly damaging	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
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
R8062:Plod3	UTSW	5	137,019,123 (GRCm39)	missense	possibly damaging	0.87
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'- GGTGTTTGGAGCTCGATCTACC -3'
(R):5'- ATGGCAAGGACATTGGGCTC -3'

Sequencing Primer
(F):5'- AGACCTTTGTGCACCAGAG -3'
(R):5'- CATTGGGCTCAGGAAAAAGTC -3'

Posted On

2016-08-04