Mutagenetix > Incidental Mutation

Incidental Mutation 'R8304:P3h1'

639375

Institutional Source

Beutler Lab

Gene Symbol

P3h1

Ensembl Gene

ENSMUSG00000028641

Gene Name

prolyl 3-hydroxylase 1

Synonyms

2410024C15Rik, Lepre1, Leprecan, Gros1

MMRRC Submission

067791-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8304 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

119090112-119106172 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 119104402 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Methionine at position 641 (T641M)

Ref Sequence

ENSEMBL: ENSMUSP00000112504 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030393] [ENSMUST00000081606] [ENSMUST00000102662] [ENSMUST00000121111] [ENSMUST00000136278]

AlphaFold

Q3V1T4

Predicted Effect

probably damaging
Transcript: ENSMUST00000030393
AA Change: T648M

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000030393
Gene: ENSMUSG00000028641
AA Change: T648M

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
low complexity region	60	84	N/A	INTRINSIC
low complexity region	117	127	N/A	INTRINSIC
internal_repeat_1	136	213	2.49e-12	PROSPERO
internal_repeat_1	294	369	2.49e-12	PROSPERO
Blast:P4Hc	419	462	2e-14	BLAST
P4Hc	479	687	5.96e-53	SMART
low complexity region	714	725	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000081606
AA Change: T462M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000080312
Gene: ENSMUSG00000028641
AA Change: T462M

Domain	Start	End	E-Value	Type
SCOP:d1hxia_	80	195	4e-5	SMART
Blast:P4Hc	125	206	2e-11	BLAST
Blast:P4Hc	233	276	1e-14	BLAST
P4Hc	293	501	5.96e-53	SMART
low complexity region	528	539	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000102662
AA Change: T641M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000099723
Gene: ENSMUSG00000028641
AA Change: T641M

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
low complexity region	60	84	N/A	INTRINSIC
low complexity region	117	127	N/A	INTRINSIC
internal_repeat_1	136	213	1.9e-12	PROSPERO
internal_repeat_1	294	369	1.9e-12	PROSPERO
Blast:P4Hc	412	455	2e-14	BLAST
P4Hc	472	680	5.96e-53	SMART
low complexity region	707	718	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000121111
AA Change: T641M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000112504
Gene: ENSMUSG00000028641
AA Change: T641M

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
low complexity region	60	84	N/A	INTRINSIC
low complexity region	117	127	N/A	INTRINSIC
internal_repeat_1	136	213	2.32e-12	PROSPERO
internal_repeat_1	294	369	2.32e-12	PROSPERO
Blast:P4Hc	412	455	2e-14	BLAST
P4Hc	472	680	5.96e-53	SMART
low complexity region	707	718	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000136278

SMART Domains

Protein: ENSMUSP00000119695
Gene: ENSMUSG00000028641

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
low complexity region	60	84	N/A	INTRINSIC
low complexity region	117	127	N/A	INTRINSIC
internal_repeat_1	136	198	6.76e-13	PROSPERO
internal_repeat_1	294	356	6.76e-13	PROSPERO

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

98% (58/59)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an enzyme that is a member of the collagen prolyl hydroxylase family. These enzymes are localized to the endoplasmic reticulum and their activity is required for proper collagen synthesis and assembly. Mutations in this gene are associated with osteogenesis imperfecta type VIII. Three alternatively spliced transcript variants encoding different isoforms have been described. Other variants may exist, but their biological validity has not been determined. [provided by RefSeq, Aug 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced size, disproportional reduction in long bone length, decreased bone density, decreased bone mineral density, reduced body fat, delayed ossification, and abnormal collagen networks in the skin and tendons. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	A	G	11: 109,997,954 (GRCm39)		probably null	Het
Akap11	T	C	14: 78,750,672 (GRCm39)	T572A		Het
Amigo2	A	T	15: 97,144,038 (GRCm39)	L128Q	probably damaging	Het
Ankrd12	A	G	17: 66,291,542 (GRCm39)	I1297T	possibly damaging	Het
Arhgap32	T	A	9: 32,167,233 (GRCm39)	C623*	probably null	Het
Armc2	T	C	10: 41,823,935 (GRCm39)	Y511C	probably damaging	Het
Asb15	C	T	6: 24,559,296 (GRCm39)	P147L	possibly damaging	Het
Caprin1	G	T	2: 103,599,862 (GRCm39)	N604K	probably damaging	Het
Ccnl2	T	C	4: 155,897,679 (GRCm39)	F113L	probably benign	Het
Cltc	C	T	11: 86,616,087 (GRCm39)	R393H	probably benign	Het
Cul4a	G	A	8: 13,177,727 (GRCm39)	C289Y	possibly damaging	Het
Cyp4a29	T	A	4: 115,111,653 (GRCm39)	F477I	probably damaging	Het
Dapk2	C	T	9: 66,139,027 (GRCm39)	A116V	possibly damaging	Het
Ddx60	T	C	8: 62,451,803 (GRCm39)	I1231T	possibly damaging	Het
Eif5b	A	G	1: 38,084,774 (GRCm39)	I874V	probably benign	Het
Eral1	A	T	11: 77,966,828 (GRCm39)	S196T	probably damaging	Het
Erc2	T	G	14: 27,375,122 (GRCm39)	D113E	probably damaging	Het
Frmpd2	A	G	14: 33,274,066 (GRCm39)	I1103V	possibly damaging	Het
Galm	A	G	17: 80,490,766 (GRCm39)	T308A	probably damaging	Het
Helz2	A	T	2: 180,871,950 (GRCm39)	N2650K	probably benign	Het
Herc2	A	G	7: 55,809,186 (GRCm39)	D2562G	probably damaging	Het
Hmmr	G	A	11: 40,612,499 (GRCm39)	S206F	probably damaging	Het
Hspbap1	T	A	16: 35,607,695 (GRCm39)	L67*	probably null	Het
Irx3	T	A	8: 92,526,834 (GRCm39)	D290V	probably damaging	Het
Kcns1	A	T	2: 164,010,022 (GRCm39)	Y246N	probably damaging	Het
Kidins220	A	G	12: 25,107,127 (GRCm39)	T1557A	probably benign	Het
Lrriq1	T	C	10: 103,069,929 (GRCm39)	N29S	possibly damaging	Het
Mmp24	T	C	2: 155,641,759 (GRCm39)	F196L	possibly damaging	Het
Mroh2b	T	C	15: 4,955,119 (GRCm39)	V704A	probably damaging	Het
Mst1	A	G	9: 107,958,803 (GRCm39)	M112V	probably benign	Het
Myh8	C	A	11: 67,195,162 (GRCm39)	H1659N	possibly damaging	Het
Nlgn1	C	T	3: 26,187,534 (GRCm39)	C117Y	probably damaging	Het
Opa1	C	T	16: 29,416,489 (GRCm39)	T237M	possibly damaging	Het
Or2r2	C	T	6: 42,463,672 (GRCm39)	V152I	probably benign	Het
Or51f5	A	G	7: 102,423,917 (GRCm39)	Y62C	possibly damaging	Het
Or5v1	A	T	17: 37,810,261 (GRCm39)	T240S	probably damaging	Het
Or8b57	A	T	9: 40,003,650 (GRCm39)	I204N	probably damaging	Het
Pak5	T	C	2: 135,940,203 (GRCm39)	H537R	probably benign	Het
Ppp1r12b	A	T	1: 134,824,101 (GRCm39)	L174Q	possibly damaging	Het
Prkg1	A	G	19: 30,701,584 (GRCm39)	V326A	possibly damaging	Het
Psmb3	T	A	11: 97,601,995 (GRCm39)	C122S	probably benign	Het
Sh3bgrl3	C	A	4: 133,855,312 (GRCm39)	A45S	probably benign	Het
Slc25a47	T	C	12: 108,821,868 (GRCm39)	V219A	possibly damaging	Het
Slfn9	A	C	11: 82,873,605 (GRCm39)	S433A	probably benign	Het
Spata13	A	T	14: 60,993,957 (GRCm39)	R1136S	possibly damaging	Het
Stab1	C	A	14: 30,870,911 (GRCm39)	A1313S	probably benign	Het
Stim1	G	A	7: 102,084,688 (GRCm39)	A547T	possibly damaging	Het
Taf5l	A	T	8: 124,730,251 (GRCm39)	I146N	probably benign	Het
Tbc1d12	A	T	19: 38,825,824 (GRCm39)	E225V	possibly damaging	Het
Tesc	T	C	5: 118,194,495 (GRCm39)	Y135H	probably benign	Het
Tfg	T	C	16: 56,521,581 (GRCm39)	E145G	possibly damaging	Het
Tg	T	A	15: 66,565,109 (GRCm39)	C1150*	probably null	Het
Tmtc1	T	C	6: 148,172,883 (GRCm39)	N616S	probably damaging	Het
Trpm7	A	T	2: 126,639,797 (GRCm39)	W1600R	probably damaging	Het
Ttc17	A	T	2: 94,199,526 (GRCm39)		probably benign	Het
Zfand1	A	T	3: 10,413,615 (GRCm39)	L24*	probably null	Het
Zfp282	AGCGGCGGCGGCGGCGGC	AGCGGCGGCGGCGGC	6: 47,881,722 (GRCm39)		probably benign	Het
Zfp770	A	C	2: 114,027,891 (GRCm39)	F59L	probably damaging	Het

Other mutations in P3h1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01622:P3h1	APN	4	119,092,480 (GRCm39)	missense	probably damaging	1.00
IGL01623:P3h1	APN	4	119,092,480 (GRCm39)	missense	probably damaging	1.00
IGL01645:P3h1	APN	4	119,093,980 (GRCm39)	missense	probably damaging	1.00
IGL02140:P3h1	APN	4	119,095,062 (GRCm39)	missense	probably damaging	1.00
IGL02415:P3h1	APN	4	119,105,152 (GRCm39)	missense	probably benign
IGL02543:P3h1	APN	4	119,095,053 (GRCm39)	splice site	probably benign
IGL02870:P3h1	APN	4	119,104,768 (GRCm39)	missense	probably damaging	1.00
IGL02972:P3h1	APN	4	119,105,157 (GRCm39)	missense	possibly damaging	0.75
IGL03067:P3h1	APN	4	119,092,477 (GRCm39)	missense	probably damaging	0.99
IGL03077:P3h1	APN	4	119,093,983 (GRCm39)	missense	probably damaging	1.00
woohoo	UTSW	4	119,098,329 (GRCm39)	nonsense	probably null
R0194:P3h1	UTSW	4	119,095,149 (GRCm39)	missense	probably damaging	1.00
R0523:P3h1	UTSW	4	119,098,727 (GRCm39)	missense	probably benign	0.32
R0734:P3h1	UTSW	4	119,095,885 (GRCm39)	missense	probably damaging	1.00
R0944:P3h1	UTSW	4	119,095,956 (GRCm39)	missense	probably benign	0.00
R1018:P3h1	UTSW	4	119,095,104 (GRCm39)	missense	probably damaging	0.99
R1978:P3h1	UTSW	4	119,105,173 (GRCm39)	missense	probably null	0.00
R2697:P3h1	UTSW	4	119,104,377 (GRCm39)	missense	probably damaging	1.00
R5668:P3h1	UTSW	4	119,101,243 (GRCm39)	missense	possibly damaging	0.89
R5750:P3h1	UTSW	4	119,095,863 (GRCm39)	missense	probably damaging	0.96
R5965:P3h1	UTSW	4	119,105,424 (GRCm39)	missense	probably benign	0.00
R5987:P3h1	UTSW	4	119,103,862 (GRCm39)	missense	probably damaging	1.00
R6111:P3h1	UTSW	4	119,098,329 (GRCm39)	nonsense	probably null
R6786:P3h1	UTSW	4	119,095,151 (GRCm39)	missense	possibly damaging	0.65
R7142:P3h1	UTSW	4	119,104,358 (GRCm39)	missense	probably benign	0.00
R8068:P3h1	UTSW	4	119,094,059 (GRCm39)	missense	probably damaging	1.00
R9502:P3h1	UTSW	4	119,094,008 (GRCm39)	missense	possibly damaging	0.86
R9680:P3h1	UTSW	4	119,090,428 (GRCm39)	missense	probably benign	0.17

Predicted Primers

PCR Primer
(F):5'- GGCTGGGTTTGACACAAAGG -3'
(R):5'- AGCCTCAGAAGAGCAATGGATC -3'

Sequencing Primer
(F):5'- CTGGGTTTGACACAAAGGTATGC -3'
(R):5'- TGGATCATTAGGACAAAGACCC -3'

Posted On

2020-07-28