Mutagenetix > Incidental Mutation

Incidental Mutation 'R5012:Lamtor2'

390564

Institutional Source

Beutler Lab

Gene Symbol

Lamtor2

Ensembl Gene

ENSMUSG00000028062

Gene Name

late endosomal/lysosomal adaptor, MAPK and MTOR activator 2

Synonyms

2010111E04Rik, Robld3, Mapbpip, Rab25, P14

MMRRC Submission

042603-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5012 (G1)

Quality Score

218

Status

Validated

Chromosome

Chromosomal Location

88457126-88460258 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 88460163 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 3 (R3H)

Ref Sequence

ENSEMBL: ENSMUSP00000029698 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000008745] [ENSMUST00000008748] [ENSMUST00000029698] [ENSMUST00000119002] [ENSMUST00000131775] [ENSMUST00000192962]

AlphaFold

Q9JHS3

PDB Structure

MP1-p14 Complex [X-RAY DIFFRACTION]
Structure of the Adaptor Protein p14 reveals a Profilin-like Fold with Novel Function [SOLUTION NMR]
Crystal Structure of p14/MP1 at 1.9 A resolution [X-RAY DIFFRACTION]
Crystal structure of the p14/MP1 complex at 2.15 A resolution [X-RAY DIFFRACTION]
MP1-p14 Scaffolding complex [X-RAY DIFFRACTION]
MP1-p14 Scaffolding complex [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000008745

SMART Domains

Protein: ENSMUSP00000008745
Gene: ENSMUSG00000008601

Domain	Start	End	E-Value	Type
RAB	13	176	2.1e-95	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000008748

SMART Domains

Protein: ENSMUSP00000008748
Gene: ENSMUSG00000008604

Domain	Start	End	E-Value	Type
UBQ	13	83	9.08e-17	SMART
low complexity region	93	119	N/A	INTRINSIC
low complexity region	130	149	N/A	INTRINSIC
low complexity region	152	170	N/A	INTRINSIC
low complexity region	176	185	N/A	INTRINSIC
STI1	187	224	2.76e-6	SMART
STI1	225	256	2.39e-1	SMART
low complexity region	302	313	N/A	INTRINSIC
low complexity region	323	335	N/A	INTRINSIC
low complexity region	339	351	N/A	INTRINSIC
STI1	388	435	7.4e-7	SMART
STI1	439	471	3.21e1	SMART
low complexity region	528	539	N/A	INTRINSIC
UBA	554	592	8.25e-7	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029698
AA Change: R3H

PolyPhen 2 Score 0.594 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000029698
Gene: ENSMUSG00000028062
AA Change: R3H

Domain	Start	End	E-Value	Type
Robl_LC7	7	95	2.65e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000119002

SMART Domains

Protein: ENSMUSP00000112936
Gene: ENSMUSG00000028062

Domain	Start	End	E-Value	Type
Blast:Robl_LC7	1	22	2e-8	BLAST
PDB:3CPT\|B	1	52	2e-32	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000131775

SMART Domains

Protein: ENSMUSP00000120505
Gene: ENSMUSG00000008601

Domain	Start	End	E-Value	Type
RAB	3	122	6.15e-47	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145172

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145548

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156421

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149724

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194303

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192687

Predicted Effect

probably benign
Transcript: ENSMUST00000192962

Meta Mutation Damage Score

0.1220

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.9%
20x: 90.9%

Validation Efficiency

98% (45/46)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The product of this gene is highly conserved with a mouse protein associated with the cytoplasmic face of late endosomes and lysosomes. The mouse protein interacts with MAPK scaffold protein 1, a component of the mitogen-activated protein kinase pathway. In humans, a mutation in this gene has been associated with a primary immunodeficiency syndrome, and suggests a role for this protein in endosomal biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]
PHENOTYPE: Embryos homozygous for a knock-out allele display severe developmental defects, are growth retarded and die prior to E10.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 37 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810055G02Rik	C	A	19: 3,767,217 (GRCm39)	T268K	possibly damaging	Het
2700049A03Rik	G	T	12: 71,211,320 (GRCm39)	E685*	probably null	Het
2700049A03Rik	A	T	12: 71,211,321 (GRCm39)	E685V	possibly damaging	Het
Acsl1	A	G	8: 46,974,468 (GRCm39)	S314G	probably benign	Het
Aftph	G	A	11: 20,648,264 (GRCm39)		probably benign	Het
Ankrd34c	T	G	9: 89,611,709 (GRCm39)	I211L	probably benign	Het
Anks1b	A	G	10: 90,194,999 (GRCm39)	T560A	probably benign	Het
Carmil1	G	T	13: 24,208,403 (GRCm39)	S1247R	possibly damaging	Het
Elf1	T	A	14: 79,808,174 (GRCm39)	Y172N	probably damaging	Het
Emx1	C	T	6: 85,180,955 (GRCm39)	P224L	probably benign	Het
Fastkd2	A	T	1: 63,789,055 (GRCm39)		probably benign	Het
Fbxw27	C	A	9: 109,602,271 (GRCm39)	C234F	probably benign	Het
Grn	C	A	11: 102,321,380 (GRCm39)		probably benign	Het
Igkv6-23	C	A	6: 70,237,529 (GRCm39)	A71S	probably damaging	Het
Igsf10	A	G	3: 59,226,143 (GRCm39)	L2510P	probably damaging	Het
Itgal	T	C	7: 126,898,802 (GRCm39)		probably null	Het
Kmt2c	C	A	5: 25,504,710 (GRCm39)	G122*	probably null	Het
Magi2	A	T	5: 20,670,618 (GRCm39)	T321S	probably damaging	Het
Mau2	A	G	8: 70,484,107 (GRCm39)		probably null	Het
Mcm7	A	T	5: 138,167,609 (GRCm39)		probably null	Het
Mitd1	A	T	1: 37,924,374 (GRCm39)	C59S	probably benign	Het
Muc6	A	G	7: 141,216,570 (GRCm39)	L2636P	possibly damaging	Het
Paip1	A	G	13: 119,584,338 (GRCm39)	M233V	probably benign	Het
Pcdhb11	C	A	18: 37,556,029 (GRCm39)	T453N	possibly damaging	Het
Plcb1	A	G	2: 135,175,320 (GRCm39)	N545S	probably null	Het
Prl8a9	A	T	13: 27,746,594 (GRCm39)		probably null	Het
Psmc2	A	G	5: 22,007,563 (GRCm39)	T308A	probably benign	Het
Rassf2	C	A	2: 131,851,610 (GRCm39)	R44L	probably damaging	Het
Scn11a	A	T	9: 119,609,944 (GRCm39)	M968K	probably benign	Het
Septin4	T	A	11: 87,475,230 (GRCm39)	S146T	possibly damaging	Het
Slc41a2	A	G	10: 83,137,127 (GRCm39)	I260T	probably benign	Het
Steap2	G	C	5: 5,727,784 (GRCm39)	L184V	possibly damaging	Het
Ttll5	G	A	12: 85,973,618 (GRCm39)	E776K	possibly damaging	Het
Vipr1	A	T	9: 121,487,111 (GRCm39)		probably null	Het
Yars2	T	C	16: 16,121,448 (GRCm39)	S201P	probably damaging	Het
Zfp386	T	A	12: 116,022,864 (GRCm39)	I194K	probably benign	Het
Zfp988	A	G	4: 147,416,060 (GRCm39)	I165V	probably benign	Het

Other mutations in Lamtor2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
Blaze	UTSW	3	88,460,163 (GRCm39)	missense	possibly damaging	0.59
R5678:Lamtor2	UTSW	3	88,458,101 (GRCm39)	unclassified	probably benign
R6265:Lamtor2	UTSW	3	88,458,020 (GRCm39)	nonsense	probably null
R6983:Lamtor2	UTSW	3	88,460,146 (GRCm39)	nonsense	probably null
R7903:Lamtor2	UTSW	3	88,459,817 (GRCm39)	missense	possibly damaging	0.90

Predicted Primers

PCR Primer
(F):5'- GCTTGCAACATTAGCCACCTC -3'
(R):5'- CTATGGTTCCCAGAATTCCTTGAG -3'

Sequencing Primer
(F):5'- CCCGGCGTAGGGCTCTTC -3'
(R):5'- CAGAATTCCTTGAGCGATCACATG -3'

Posted On

2016-06-06