Mutagenetix > Incidental Mutation

Incidental Mutation 'R1501:Plekhm1'

169290

Institutional Source

Beutler Lab

Gene Symbol

Plekhm1

Ensembl Gene

ENSMUSG00000034247

Gene Name

pleckstrin homology domain containing, family M (with RUN domain) member 1

Synonyms

AP162, B2, D330036J23Rik

MMRRC Submission

040867-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1501 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

103255101-103303513 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 103277888 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 403 (S403P)

Ref Sequence

ENSEMBL: ENSMUSP00000047327 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041272]

AlphaFold

Q7TSI1

Predicted Effect

probably benign
Transcript: ENSMUST00000041272
AA Change: S403P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000047327
Gene: ENSMUSG00000034247
AA Change: S403P

Domain	Start	End	E-Value	Type
RUN	117	180	3.36e-20	SMART
low complexity region	246	273	N/A	INTRINSIC
low complexity region	336	350	N/A	INTRINSIC
low complexity region	361	373	N/A	INTRINSIC
Blast:DUF4206	448	543	2e-11	BLAST
PH	552	644	2.16e-9	SMART
low complexity region	658	674	N/A	INTRINSIC
PH	702	797	2.15e-4	SMART
DUF4206	864	1068	7.51e-103	SMART
C1	1005	1058	2.72e-3	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000184350

Coding Region Coverage

1x: 99.4%
3x: 98.7%
10x: 97.4%
20x: 95.7%

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 essential for bone resorption, and may play a critical role in vesicular transport in the osteoclast. Mutations in this gene are associated with autosomal recessive osteopetrosis type 6 (OPTB6). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit increased trabecular bone mass and decreased bone resorption capacity of osteoclasts caused by defects in the peripheral positioning and secretion of lysosomes. Mice homozygous for a gene trap insertion do not exhibit any detectable phenotype. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akap11	A	T	14: 78,750,787 (GRCm39)	S533R	probably benign	Het
Amph	C	T	13: 19,288,461 (GRCm39)	Q317*	probably null	Het
Bach2	A	G	4: 32,562,279 (GRCm39)	T249A	possibly damaging	Het
Cacna2d3	A	G	14: 28,703,137 (GRCm39)	C845R	probably damaging	Het
Calml4	A	G	9: 62,778,622 (GRCm39)	K12E	probably benign	Het
Chrd	C	T	16: 20,556,283 (GRCm39)	R615W	probably damaging	Het
Chst15	T	A	7: 131,870,798 (GRCm39)	K246*	probably null	Het
Cmtr2	G	A	8: 110,948,235 (GRCm39)	D182N	probably benign	Het
Cyp2d9	C	A	15: 82,338,525 (GRCm39)	C186*	probably null	Het
Cyp3a13	G	T	5: 137,909,892 (GRCm39)		probably null	Het
Dcaf17	A	T	2: 70,912,332 (GRCm39)	I320F	probably damaging	Het
Ddx10	T	C	9: 53,145,297 (GRCm39)	I227V	possibly damaging	Het
Dlc1	G	T	8: 37,405,302 (GRCm39)	N162K	probably benign	Het
Dnhd1	G	A	7: 105,317,670 (GRCm39)	R455H	probably benign	Het
Drg2	G	T	11: 60,355,679 (GRCm39)	A306S	probably benign	Het
Dsg1a	A	T	18: 20,465,076 (GRCm39)	R422S	probably damaging	Het
Ehbp1l1	A	G	19: 5,766,452 (GRCm39)	V353A	probably damaging	Het
Emilin2	T	C	17: 71,617,756 (GRCm39)	S34G	probably benign	Het
Enpp2	C	A	15: 54,702,910 (GRCm39)	W862L	probably damaging	Het
Exoc2	T	C	13: 31,119,485 (GRCm39)	I139V	probably benign	Het
Fhad1	C	T	4: 141,691,936 (GRCm39)	R400H	probably benign	Het
Fv1	C	T	4: 147,954,595 (GRCm39)	T387M	probably damaging	Het
Gatad1	T	A	5: 3,693,701 (GRCm39)	D156V	probably damaging	Het
Gm4744	A	G	6: 40,927,367 (GRCm39)		probably benign	Het
Gm4799	G	A	10: 82,790,469 (GRCm39)		noncoding transcript	Het
Hadha	A	G	5: 30,333,804 (GRCm39)	F405S	probably benign	Het
Ifit3	T	C	19: 34,565,651 (GRCm39)	V399A	probably benign	Het
Il1rapl1	G	T	X: 86,348,469 (GRCm39)	Y150*	probably null	Het
Kirrel1	T	C	3: 86,997,779 (GRCm39)	E248G	probably benign	Het
Krt72	C	A	15: 101,686,769 (GRCm39)	K392N	probably damaging	Het
Loxhd1	G	A	18: 77,444,528 (GRCm39)	G309D	probably damaging	Het
Mc3r	T	G	2: 172,091,300 (GRCm39)	I174S	probably benign	Het
Me3	A	G	7: 89,282,273 (GRCm39)	D52G	probably benign	Het
Med12l	T	C	3: 59,168,256 (GRCm39)		probably null	Het
Mgat5	G	A	1: 127,325,378 (GRCm39)		probably null	Het
Mphosph10	A	T	7: 64,039,252 (GRCm39)	F239L	probably damaging	Het
Mrps7	T	C	11: 115,495,023 (GRCm39)	S13P	probably benign	Het
Nexn	T	C	3: 151,943,323 (GRCm39)	T527A	possibly damaging	Het
Nlrp1b	G	A	11: 71,046,885 (GRCm39)	H1156Y	probably damaging	Het
Nostrin	A	G	2: 68,989,129 (GRCm39)	E120G	probably damaging	Het
Nsun2	A	G	13: 69,779,706 (GRCm39)	E624G	probably damaging	Het
Oga	T	C	19: 45,767,079 (GRCm39)	D99G	probably null	Het
Or4c102	G	A	2: 88,422,492 (GRCm39)	V115I	possibly damaging	Het
Or4k2	A	G	14: 50,424,539 (GRCm39)	I45T	probably damaging	Het
Or52n4b	G	A	7: 108,143,782 (GRCm39)	V15I	probably benign	Het
Or5p70	A	C	7: 107,995,289 (GRCm39)	K321Q	probably benign	Het
Phldb2	T	C	16: 45,598,146 (GRCm39)	N802S	probably damaging	Het
Pik3c2g	T	C	6: 139,789,796 (GRCm39)		probably null	Het
Pikfyve	T	A	1: 65,304,443 (GRCm39)	I1670N	possibly damaging	Het
Pld5	A	G	1: 175,803,087 (GRCm39)	F393L	probably benign	Het
Plekhg1	C	A	10: 3,907,361 (GRCm39)	D759E	probably benign	Het
Pop1	T	C	15: 34,510,503 (GRCm39)	F432L	probably benign	Het
Ptpn13	T	C	5: 103,664,230 (GRCm39)	I406T	probably benign	Het
Ptpn5	G	T	7: 46,739,623 (GRCm39)	D185E	probably benign	Het
Rad50	G	T	11: 53,578,978 (GRCm39)	Q527K	possibly damaging	Het
Scn7a	A	G	2: 66,530,507 (GRCm39)	F613L	probably benign	Het
Sec16a	T	A	2: 26,330,057 (GRCm39)	M653L	probably benign	Het
Sh3bp2	T	C	5: 34,712,920 (GRCm39)		probably null	Het
Slc22a3	G	A	17: 12,725,991 (GRCm39)	T74I	probably benign	Het
Slc23a4	A	G	6: 34,932,057 (GRCm39)	L272P	probably damaging	Het
Slc26a8	T	C	17: 28,857,536 (GRCm39)	D869G	possibly damaging	Het
Slc5a11	T	A	7: 122,859,731 (GRCm39)	V291E	probably damaging	Het
Slc6a19	C	A	13: 73,832,167 (GRCm39)	A470S	probably benign	Het
Slfn8	A	G	11: 82,894,006 (GRCm39)	S878P	probably damaging	Het
Smchd1	A	G	17: 71,672,089 (GRCm39)	M1655T	possibly damaging	Het
Srgap2	A	G	1: 131,220,437 (GRCm39)	L179P	probably damaging	Het
Tbx2	A	G	11: 85,725,622 (GRCm39)	D191G	probably damaging	Het
Tenm3	A	G	8: 48,796,351 (GRCm39)	Y485H	probably damaging	Het
Trim12c	T	A	7: 103,990,095 (GRCm39)		probably benign	Het
Trpc6	A	G	9: 8,610,170 (GRCm39)	T213A	probably damaging	Het
Upp1	T	A	11: 9,084,708 (GRCm39)		probably null	Het
Vmn1r46	A	T	6: 89,953,198 (GRCm39)	I16L	probably benign	Het
Vmn2r75	A	T	7: 85,814,850 (GRCm39)	D214E	possibly damaging	Het
Vmn2r95	T	A	17: 18,660,118 (GRCm39)	Y177N	probably damaging	Het
Vmn2r99	T	G	17: 19,582,521 (GRCm39)	I42S	possibly damaging	Het
Zeb1	A	T	18: 5,761,399 (GRCm39)	K232N	possibly damaging	Het
Zfp280b	T	C	10: 75,875,603 (GRCm39)	I494T	probably damaging	Het
Zfp804a	A	G	2: 82,066,143 (GRCm39)	D38G	probably damaging	Het

Other mutations in Plekhm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01517:Plekhm1	APN	11	103,285,609 (GRCm39)	missense	possibly damaging	0.54
IGL01876:Plekhm1	APN	11	103,267,577 (GRCm39)	missense	probably damaging	1.00
IGL02159:Plekhm1	APN	11	103,271,057 (GRCm39)	missense	probably benign	0.04
IGL02404:Plekhm1	APN	11	103,285,824 (GRCm39)	missense	probably benign	0.18
IGL02537:Plekhm1	APN	11	103,288,018 (GRCm39)	missense	probably damaging	1.00
IGL02568:Plekhm1	APN	11	103,285,876 (GRCm39)	missense	probably damaging	1.00
IGL02660:Plekhm1	APN	11	103,264,920 (GRCm39)	splice site	probably benign
IGL03130:Plekhm1	APN	11	103,268,207 (GRCm39)	missense	probably benign	0.17
IGL03208:Plekhm1	APN	11	103,267,596 (GRCm39)	missense	probably benign	0.00
R0442:Plekhm1	UTSW	11	103,288,000 (GRCm39)	missense	possibly damaging	0.45
R0491:Plekhm1	UTSW	11	103,285,602 (GRCm39)	missense	probably benign	0.05
R0520:Plekhm1	UTSW	11	103,285,770 (GRCm39)	missense	probably benign	0.17
R0964:Plekhm1	UTSW	11	103,285,908 (GRCm39)	nonsense	probably null
R1189:Plekhm1	UTSW	11	103,277,888 (GRCm39)	missense	probably benign	0.00
R1697:Plekhm1	UTSW	11	103,267,710 (GRCm39)	missense	probably damaging	1.00
R1781:Plekhm1	UTSW	11	103,285,682 (GRCm39)	missense	probably damaging	1.00
R1873:Plekhm1	UTSW	11	103,264,824 (GRCm39)	missense	probably benign	0.01
R2087:Plekhm1	UTSW	11	103,287,851 (GRCm39)	critical splice donor site	probably null
R2215:Plekhm1	UTSW	11	103,267,811 (GRCm39)	missense	probably damaging	1.00
R2271:Plekhm1	UTSW	11	103,277,948 (GRCm39)	missense	probably benign	0.00
R4256:Plekhm1	UTSW	11	103,261,760 (GRCm39)	missense	probably damaging	0.98
R4393:Plekhm1	UTSW	11	103,267,791 (GRCm39)	missense	possibly damaging	0.51
R4526:Plekhm1	UTSW	11	103,286,130 (GRCm39)	missense	probably damaging	0.97
R5119:Plekhm1	UTSW	11	103,278,141 (GRCm39)	missense	possibly damaging	0.62
R5975:Plekhm1	UTSW	11	103,267,517 (GRCm39)	missense	possibly damaging	0.49
R6389:Plekhm1	UTSW	11	103,257,720 (GRCm39)	missense	probably benign	0.21
R6454:Plekhm1	UTSW	11	103,268,208 (GRCm39)	missense	probably damaging	1.00
R6755:Plekhm1	UTSW	11	103,278,069 (GRCm39)	missense	possibly damaging	0.65
R6830:Plekhm1	UTSW	11	103,267,715 (GRCm39)	missense	probably damaging	0.97
R7039:Plekhm1	UTSW	11	103,286,054 (GRCm39)	missense	probably damaging	1.00
R7066:Plekhm1	UTSW	11	103,261,814 (GRCm39)	missense	possibly damaging	0.47
R7149:Plekhm1	UTSW	11	103,285,742 (GRCm39)	missense	probably damaging	0.98
R7349:Plekhm1	UTSW	11	103,278,160 (GRCm39)	missense	probably damaging	0.98
R7505:Plekhm1	UTSW	11	103,270,855 (GRCm39)	splice site	probably null
R7792:Plekhm1	UTSW	11	103,287,886 (GRCm39)	missense	probably damaging	0.99
R7867:Plekhm1	UTSW	11	103,271,153 (GRCm39)	missense	probably damaging	1.00
R8124:Plekhm1	UTSW	11	103,257,775 (GRCm39)	missense	probably benign	0.02
R8194:Plekhm1	UTSW	11	103,285,886 (GRCm39)	missense	possibly damaging	0.68
R8725:Plekhm1	UTSW	11	103,258,444 (GRCm39)	missense	probably damaging	1.00
R8727:Plekhm1	UTSW	11	103,258,444 (GRCm39)	missense	probably damaging	1.00
R8734:Plekhm1	UTSW	11	103,285,778 (GRCm39)	missense	probably damaging	1.00
R8927:Plekhm1	UTSW	11	103,268,039 (GRCm39)	missense	probably benign	0.04
R8928:Plekhm1	UTSW	11	103,268,039 (GRCm39)	missense	probably benign	0.04
R9681:Plekhm1	UTSW	11	103,258,950 (GRCm39)	missense	possibly damaging	0.82
X0058:Plekhm1	UTSW	11	103,268,192 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- GGGTCACCAGATGGACAAACTTCAG -3'
(R):5'- AATTCTGCACCAAGCAGCGGAC -3'

Sequencing Primer
(F):5'- CAGATGGACAAACTTCAGCTTAG -3'
(R):5'- CCCATGTTCCAGACGCC -3'

Posted On

2014-04-13