Mutagenetix > Incidental Mutation

Incidental Mutation 'R9681:Plekhm1'

728577

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9681 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

103255101-103303513 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 103258950 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 980 (V980A)

Ref Sequence

ENSEMBL: ENSMUSP00000047327 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041272] [ENSMUST00000092557]

AlphaFold

Q7TSI1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000041272
AA Change: V980A

PolyPhen 2 Score 0.824 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000047327
Gene: ENSMUSG00000034247
AA Change: V980A

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: ENSMUST00000092557

SMART Domains

Protein: ENSMUSP00000102637
Gene: ENSMUSG00000034255

Domain	Start	End	E-Value	Type
SH3	9	68	1.59e-1	SMART
low complexity region	73	89	N/A	INTRINSIC
low complexity region	220	229	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000184350

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610030E20Rik	A	G	6: 72,324,450 (GRCm39)	D20G	probably damaging	Het
Acbd3	T	A	1: 180,566,082 (GRCm39)	Y258*	probably null	Het
Adamts1	T	A	16: 85,599,498 (GRCm39)	H34L		Het
Ankmy1	G	T	1: 92,813,882 (GRCm39)	N432K	possibly damaging	Het
Ano1	A	G	7: 144,143,893 (GRCm39)	M966T	possibly damaging	Het
Ark2n	A	T	18: 77,722,989 (GRCm39)	V349D	possibly damaging	Het
C2cd3	A	G	7: 100,023,662 (GRCm39)	T83A	probably benign	Het
Cdk1	T	A	10: 69,178,449 (GRCm39)	D137V	possibly damaging	Het
Cfap299	T	A	5: 98,477,214 (GRCm39)	M1K	probably null	Het
Chia1	A	G	3: 106,037,996 (GRCm39)	Y326C	probably damaging	Het
Ciz1	A	G	2: 32,260,974 (GRCm39)	D295G	possibly damaging	Het
Clrn1	C	T	3: 58,792,251 (GRCm39)	V71I	probably benign	Het
Cr1l	T	C	1: 194,800,149 (GRCm39)	D175G	probably damaging	Het
Crem	A	T	18: 3,268,067 (GRCm39)	V87E	probably damaging	Het
Cyp2b19	T	A	7: 26,466,328 (GRCm39)	L377Q	probably benign	Het
Ddx42	T	A	11: 106,125,679 (GRCm39)	V243D	probably damaging	Het
Dnah14	T	C	1: 181,562,414 (GRCm39)	V2658A	possibly damaging	Het
Dnah3	T	G	7: 119,677,611 (GRCm39)	M437L	probably benign	Het
Flrt2	T	A	12: 95,745,425 (GRCm39)		probably benign	Het
Gm10142	T	A	10: 77,551,880 (GRCm39)	C80*	probably null	Het
Gpr158	A	G	2: 21,831,315 (GRCm39)	E805G	probably damaging	Het
Grwd1	T	C	7: 45,479,473 (GRCm39)	E134G	probably benign	Het
Hdac11	T	A	6: 91,150,068 (GRCm39)	V289D	probably benign	Het
Hsdl1	T	C	8: 120,293,081 (GRCm39)	E118G	possibly damaging	Het
Igdcc4	T	A	9: 65,041,858 (GRCm39)	L1095Q	possibly damaging	Het
Ildr1	T	A	16: 36,528,749 (GRCm39)	C65S	probably damaging	Het
Itgal	T	C	7: 126,929,422 (GRCm39)	F1113S	probably damaging	Het
Itsn2	G	T	12: 4,683,499 (GRCm39)	V341F	unknown	Het
Jak1	G	A	4: 101,019,085 (GRCm39)	R723C	probably damaging	Het
Limch1	A	G	5: 67,126,422 (GRCm39)	T8A	probably damaging	Het
Limd1	T	A	9: 123,345,903 (GRCm39)	C561S	possibly damaging	Het
Map3k19	A	G	1: 127,750,097 (GRCm39)	F1085L	possibly damaging	Het
Mcm7	A	T	5: 138,164,220 (GRCm39)	Y600*	probably null	Het
Mecom	A	T	3: 30,033,803 (GRCm39)	D300E	probably benign	Het
Mfap4	T	A	11: 61,376,925 (GRCm39)	Y51*	probably null	Het
Mug1	T	A	6: 121,833,254 (GRCm39)	N286K	probably benign	Het
Myl2	A	T	5: 122,240,783 (GRCm39)	R40*	probably null	Het
Nom1	A	G	5: 29,642,623 (GRCm39)	S375G	probably damaging	Het
Nrcam	C	A	12: 44,598,133 (GRCm39)	P368Q	probably null	Het
Oca2	G	C	7: 55,943,623 (GRCm39)	Q265H	probably null	Het
Or52a20	T	A	7: 103,366,475 (GRCm39)	F225I	probably damaging	Het
Or52n2c	T	C	7: 104,574,075 (GRCm39)	T299A	probably damaging	Het
Or5k8	T	A	16: 58,644,176 (GRCm39)	N299Y	possibly damaging	Het
Or6c88	A	T	10: 129,406,664 (GRCm39)	T47S	probably damaging	Het
Or7a41	G	A	10: 78,871,577 (GRCm39)	D316N	probably benign	Het
Palmd	T	C	3: 116,717,120 (GRCm39)	E459G	probably benign	Het
Pde1a	G	T	2: 79,695,465 (GRCm39)	A494D	probably benign	Het
Pds5a	T	C	5: 65,808,587 (GRCm39)	Y428C	probably damaging	Het
Pgm2	T	C	5: 64,254,391 (GRCm39)	F59L	probably benign	Het
Polb	T	C	8: 23,118,346 (GRCm39)	D318G	possibly damaging	Het
Rasgef1c	T	A	11: 49,861,040 (GRCm39)	M335K	probably damaging	Het
Rasgrp4	T	C	7: 28,849,687 (GRCm39)	S651P	probably benign	Het
Robo3	A	C	9: 37,334,558 (GRCm39)	I624S	possibly damaging	Het
Robo3	T	A	9: 37,339,087 (GRCm39)	H290L	probably benign	Het
Rps6kl1	T	C	12: 85,183,599 (GRCm39)	H482R	probably damaging	Het
Slc26a9	A	T	1: 131,681,691 (GRCm39)	E168V	probably benign	Het
Slc3a2	T	C	19: 8,691,226 (GRCm39)		probably benign	Het
Slc4a4	A	T	5: 89,102,723 (GRCm39)	K54*	probably null	Het
Slitrk6	A	G	14: 110,988,258 (GRCm39)	L483P	probably damaging	Het
Svep1	T	A	4: 58,084,959 (GRCm39)	N1793I	probably damaging	Het
Ttn	T	C	2: 76,612,723 (GRCm39)	I17119V	possibly damaging	Het
Tulp4	T	C	17: 6,274,500 (GRCm39)	L617P	possibly damaging	Het
Uhrf1	A	G	17: 56,625,083 (GRCm39)	N542S	possibly damaging	Het
Vmn1r151	T	A	7: 22,198,368 (GRCm39)	T246S	probably damaging	Het
Vmn1r57	T	A	7: 5,224,069 (GRCm39)	V198E	probably damaging	Het
Vmn2r99	A	T	17: 19,598,889 (GRCm39)	Q191L	probably damaging	Het
Vrk3	C	T	7: 44,403,356 (GRCm39)	T39M	possibly damaging	Het
Zc3h3	C	A	15: 75,681,470 (GRCm39)	R537L	probably damaging	Het
Zfp64	A	T	2: 168,793,680 (GRCm39)	V22E	probably damaging	Het
Zwint	T	C	10: 72,493,112 (GRCm39)	L218P	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
R1501: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
X0058:Plekhm1	UTSW	11	103,268,192 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CCTGGTTAGTCAAGAGGTGG -3'
(R):5'- TCAAGTGTCCTAGGCAGCTC -3'

Sequencing Primer
(F):5'- CTGGTTAGTCAAGAGGTGGAGGAC -3'
(R):5'- AGACTGACTTGAACCCTTGG -3'

Posted On

2022-10-06