Mutagenetix > Incidental Mutation

Incidental Mutation 'R7903:Lamtor2'

610072

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

045955-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7903 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

88457126-88460258 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 88459817 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 26 (N26D)

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: N26D

PolyPhen 2 Score 0.902 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000029698
Gene: ENSMUSG00000028062
AA Change: N26D

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

probably benign
Transcript: ENSMUST00000192962

Coding Region Coverage

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

Validation Efficiency

100% (67/67)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700062C07Rik	T	C	18: 24,608,783 (GRCm39)		probably null	Het
Acsm2	A	T	7: 119,195,215 (GRCm39)	T596S	probably benign	Het
Aggf1	T	C	13: 95,492,966 (GRCm39)	K548E	probably damaging	Het
Anapc15	T	G	7: 101,547,193 (GRCm39)	V23G	probably benign	Het
Atp10a	T	C	7: 58,308,570 (GRCm39)	L123P	probably damaging	Het
Brf2	G	A	8: 27,616,121 (GRCm39)	T88M	possibly damaging	Het
C1ra	G	A	6: 124,494,684 (GRCm39)	E316K	probably benign	Het
Ccdc14	A	T	16: 34,525,280 (GRCm39)	H191L	probably damaging	Het
Cdc42bpg	T	A	19: 6,363,499 (GRCm39)	V453E	possibly damaging	Het
Corin	T	C	5: 72,458,843 (GRCm39)	K1110E	probably benign	Het
Cubn	T	C	2: 13,473,680 (GRCm39)	D421G	probably damaging	Het
D130043K22Rik	T	G	13: 25,059,995 (GRCm39)	V622G	probably damaging	Het
Ddb1	T	C	19: 10,585,712 (GRCm39)	V142A	probably benign	Het
Dnah3	A	G	7: 119,641,351 (GRCm39)	S1190P	probably damaging	Het
Eif4a3l2	A	G	6: 116,528,212 (GRCm39)	T30A	probably benign	Het
Elavl1	T	C	8: 4,351,756 (GRCm39)	K120R	probably benign	Het
Epb41l3	T	A	17: 69,581,332 (GRCm39)		probably null	Het
Fubp1	G	A	3: 151,920,498 (GRCm39)	W79*	probably null	Het
Gsto2	T	A	19: 47,873,096 (GRCm39)	I157N	possibly damaging	Het
Gucy2d	A	G	7: 98,108,272 (GRCm39)	D735G	probably damaging	Het
H2-D1	A	T	17: 35,482,967 (GRCm39)	I166F	probably damaging	Het
Hars2	C	A	18: 36,919,245 (GRCm39)	R128S	probably damaging	Het
Igf1r	T	C	7: 67,834,500 (GRCm39)	F496S	probably damaging	Het
Inf2	T	C	12: 112,578,988 (GRCm39)	V1256A	unknown	Het
Kif19b	T	C	5: 140,461,767 (GRCm39)	V523A	probably damaging	Het
Krt34	A	T	11: 99,932,321 (GRCm39)	M1K	probably null	Het
Map3k10	T	C	7: 27,357,382 (GRCm39)	T799A	probably damaging	Het
Map3k8	T	C	18: 4,349,162 (GRCm39)	D52G	probably benign	Het
Mcm10	T	C	2: 5,000,613 (GRCm39)	T693A	probably benign	Het
Mgarp	G	T	3: 51,304,119 (GRCm39)	A10E		Het
Mns1	A	T	9: 72,360,093 (GRCm39)	E414D	probably benign	Het
Myo16	A	G	8: 10,426,265 (GRCm39)	S341G	probably null	Het
Nags	A	T	11: 102,037,503 (GRCm39)	D198V	possibly damaging	Het
Nedd4l	C	T	18: 65,319,438 (GRCm39)	P464S	probably damaging	Het
Nicol1	T	A	5: 34,140,910 (GRCm39)		probably null	Het
Nsfl1c	T	C	2: 151,338,522 (GRCm39)	Y42H	probably damaging	Het
Obscn	T	C	11: 58,969,942 (GRCm39)	M67V	probably benign	Het
Or2b28	T	A	13: 21,532,046 (GRCm39)	I316K	probably benign	Het
Pcsk5	A	T	19: 17,549,847 (GRCm39)	L715Q	probably damaging	Het
Peg3	GTGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTC	GTGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTC	7: 6,712,167 (GRCm39)		probably benign	Het
Pfkfb4	A	T	9: 108,828,019 (GRCm39)	N64Y	probably damaging	Het
Pidd1	A	G	7: 141,019,744 (GRCm39)	F673L	probably damaging	Het
Pla2g7	A	G	17: 43,911,512 (GRCm39)		probably null	Het
Pml	T	C	9: 58,156,867 (GRCm39)	E36G	probably benign	Het
Proser1	C	A	3: 53,386,503 (GRCm39)	S795*	probably null	Het
Ptprs	T	A	17: 56,731,960 (GRCm39)	K1016*	probably null	Het
Rbfox1	T	A	16: 7,042,375 (GRCm39)	S76R	probably benign	Het
Reck	A	T	4: 43,927,166 (GRCm39)	I486F	possibly damaging	Het
Rnf103	A	T	6: 71,486,138 (GRCm39)	K256N	probably damaging	Het
Setd2	A	T	9: 110,446,905 (GRCm39)	N713I		Het
Slc38a4	C	T	15: 96,906,809 (GRCm39)	G310S	probably benign	Het
Slc7a4	C	T	16: 17,393,145 (GRCm39)	R218H	probably benign	Het
Slc7a7	T	C	14: 54,611,366 (GRCm39)	H344R	probably damaging	Het
Smarcc1	G	A	9: 110,033,334 (GRCm39)	E810K	probably benign	Het
Sord	T	A	2: 122,093,706 (GRCm39)	M275K	probably benign	Het
Spire2	C	A	8: 124,095,489 (GRCm39)	P631T	probably benign	Het
Sult6b1	T	C	17: 79,198,279 (GRCm39)	K207R	probably benign	Het
Syde2	T	A	3: 145,704,543 (GRCm39)	D498E	probably damaging	Het
Syne2	C	T	12: 76,110,958 (GRCm39)	T1024M	probably damaging	Het
Tdrd9	T	A	12: 112,018,410 (GRCm39)	D1276E	possibly damaging	Het
Tm7sf2	A	G	19: 6,121,365 (GRCm39)	F219S	probably damaging	Het
Tmcc2	C	T	1: 132,288,199 (GRCm39)	G496D	probably benign	Het
Tmtc4	G	A	14: 123,165,060 (GRCm39)	H600Y	probably benign	Het
Vmn1r224	A	T	17: 20,640,309 (GRCm39)	L295F	probably benign	Het
Vmn1r91	T	C	7: 19,835,135 (GRCm39)	I18T	possibly damaging	Het
Vwa7	G	A	17: 35,236,763 (GRCm39)	R110H	probably damaging	Het
Wbp2nl	C	T	15: 82,190,332 (GRCm39)	Q87*	probably null	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
R5012:Lamtor2	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

Predicted Primers

PCR Primer
(F):5'- ACTGAGATGGACCCTCACATAGG -3'
(R):5'- CTTCGGAAACCCTGCTTGAG -3'

Sequencing Primer
(F):5'- TTGCAAGTTCGAAGTCAGCC -3'
(R):5'- GAGGGCTTCCTCGGAAAG -3'

Posted On

2019-12-20