Mutagenetix > Incidental Mutation

Incidental Mutation 'R5431:Lhx3'

428031

Institutional Source

Beutler Lab

Gene Symbol

Lhx3

Ensembl Gene

ENSMUSG00000026934

Gene Name

LIM homeobox protein 3

Synonyms

mLim-3, Lim3, P-LIM

MMRRC Submission

042847-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5431 (G1)

Quality Score

193

Status

Not validated

Chromosome

Chromosomal Location

26200212-26208289 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 26201118 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 395 (D395G)

Ref Sequence

ENSEMBL: ENSMUSP00000028302 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028302] [ENSMUST00000054099]

AlphaFold

P50481

PDB Structure

NMR Solution Structure of a ldb1-LID:Lhx3-LIM complex [SOLUTION NMR]
Crystal Structure of Lhx3 LIM domains 1 and 2 with the binding domain of Isl1 [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000028302
AA Change: D395G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000028302
Gene: ENSMUSG00000026934
AA Change: D395G

Domain	Start	End	E-Value	Type
low complexity region	14	31	N/A	INTRINSIC
LIM	35	86	4.18e-17	SMART
LIM	94	149	7.8e-17	SMART
HOX	162	224	7.13e-23	SMART
low complexity region	237	249	N/A	INTRINSIC
low complexity region	323	342	N/A	INTRINSIC
low complexity region	353	362	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000054099
AA Change: D393G

PolyPhen 2 Score 0.635 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000056822
Gene: ENSMUSG00000026934
AA Change: D393G

Domain	Start	End	E-Value	Type
LIM	33	84	4.18e-17	SMART
LIM	92	147	7.8e-17	SMART
HOX	160	222	7.13e-23	SMART
low complexity region	235	247	N/A	INTRINSIC
low complexity region	321	340	N/A	INTRINSIC
low complexity region	351	360	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127035

SMART Domains

Protein: ENSMUSP00000134884
Gene: ENSMUSG00000026934

Domain	Start	End	E-Value	Type
Pfam:Homeobox	1	17	6.2e-5	PFAM
low complexity region	35	47	N/A	INTRINSIC
low complexity region	121	140	N/A	INTRINSIC
low complexity region	151	160	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149637

SMART Domains

Protein: ENSMUSP00000135765
Gene: ENSMUSG00000026934

Domain	Start	End	E-Value	Type
low complexity region	2	16	N/A	INTRINSIC
low complexity region	22	38	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit failure of growth and differentiation of Rathke's pouch, lack both anterior and intermediate lobes of the pituitary gland, and die perinatally, within 24 hours of birth. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310061N02Rik	T	C	16: 88,707,538 (GRCm38)	S124G	possibly damaging	Het
4921539E11Rik	T	C	4: 103,270,848 (GRCm38)	T27A	probably benign	Het
Aspg	T	A	12: 112,123,412 (GRCm38)	N461K	probably benign	Het
B4galnt3	T	A	6: 120,218,967 (GRCm38)	T300S	probably damaging	Het
BC035044	A	G	6: 128,885,007 (GRCm38)		probably benign	Het
Bmp5	C	T	9: 75,893,709 (GRCm38)	P374S	probably damaging	Het
C330018D20Rik	A	T	18: 56,957,856 (GRCm38)	F78L	probably benign	Het
Cds2	T	A	2: 132,302,170 (GRCm38)	S289T	probably benign	Het
Cerkl	C	T	2: 79,341,335 (GRCm38)	C393Y	probably damaging	Het
Cibar2	C	A	8: 120,167,303 (GRCm38)		probably null	Het
Ciita	C	T	16: 10,523,792 (GRCm38)	R1020C	probably damaging	Het
Dcaf13	C	A	15: 39,123,224 (GRCm38)	D130E	probably benign	Het
Dnal4	C	T	15: 79,762,447 (GRCm38)	G50R	probably damaging	Het
Elfn1	A	G	5: 139,971,568 (GRCm38)	N109S	probably damaging	Het
Ep400	A	G	5: 110,676,554 (GRCm38)	V2435A	unknown	Het
Fam178b	T	C	1: 36,632,485 (GRCm38)	E185G	probably damaging	Het
Fam227b	C	A	2: 126,126,931 (GRCm38)	L74F	probably benign	Het
Fgfr4	G	A	13: 55,156,651 (GRCm38)	V138I	probably benign	Het
Flnc	A	G	6: 29,456,384 (GRCm38)	I2161V	possibly damaging	Het
Frmd5	T	C	2: 121,562,909 (GRCm38)	N235S	probably damaging	Het
Gad1-ps	G	A	10: 99,445,147 (GRCm38)		noncoding transcript	Het
Ggt6	A	G	11: 72,437,738 (GRCm38)	T355A	possibly damaging	Het
Gm14393	G	A	2: 175,063,876 (GRCm38)	T41I	probably damaging	Het
Gpr151	A	C	18: 42,578,867 (GRCm38)	S249A	probably damaging	Het
Gpr152	T	A	19: 4,143,747 (GRCm38)	V429D	probably benign	Het
Grm7	G	A	6: 111,358,426 (GRCm38)	M599I	probably benign	Het
Hdac4	T	A	1: 91,972,790 (GRCm38)	R54*	probably null	Het
Ice1	A	G	13: 70,592,650 (GRCm38)	L2146S	probably damaging	Het
Igfbpl1	C	T	4: 45,815,588 (GRCm38)	V183I	probably benign	Het
Kel	G	A	6: 41,698,420 (GRCm38)	S299F	probably benign	Het
Kif14	T	C	1: 136,496,695 (GRCm38)	I1016T	possibly damaging	Het
Micu1	T	C	10: 59,750,521 (GRCm38)	Y140H	possibly damaging	Het
Myt1l	G	A	12: 29,832,332 (GRCm38)	G509R	unknown	Het
Nbn	C	T	4: 15,986,593 (GRCm38)	H665Y	probably benign	Het
Pkhd1	G	T	1: 20,117,836 (GRCm38)	T3416K	probably benign	Het
Plxnb1	T	C	9: 109,100,772 (GRCm38)	F232S	probably damaging	Het
Pus7l	T	C	15: 94,529,486 (GRCm38)	N472D	probably damaging	Het
Rfx1	C	T	8: 84,082,720 (GRCm38)	Q225*	probably null	Het
Rnase2a	T	C	14: 51,255,563 (GRCm38)	Y115C	possibly damaging	Het
Ryr1	T	A	7: 29,109,812 (GRCm38)	D386V	probably benign	Het
Sfi1	A	ATCTTCCCAAAGCCAGTGC	11: 3,153,384 (GRCm38)		probably benign	Homo
Sgcz	T	A	8: 37,639,984 (GRCm38)	T125S	probably damaging	Het
Sntb1	C	G	15: 55,642,795 (GRCm38)	G461R	probably damaging	Het
Syt2	A	G	1: 134,740,957 (GRCm38)	S36G	probably benign	Het
Tcaf3	A	G	6: 42,597,185 (GRCm38)	L31P	probably damaging	Het
Tenm3	C	A	8: 48,367,377 (GRCm38)	E142*	probably null	Het
Tgfbr2	G	T	9: 116,131,601 (GRCm38)	S94R	probably damaging	Het
Tut4	T	A	4: 108,491,412 (GRCm38)	I297N	probably damaging	Het
Vmn2r12	A	G	5: 109,091,818 (GRCm38)	I293T	probably damaging	Het
Wrap73	G	A	4: 154,145,274 (GRCm38)	R34Q	probably damaging	Het
Zc3h14	A	G	12: 98,780,065 (GRCm38)	D511G	possibly damaging	Het

Other mutations in Lhx3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02309:Lhx3	APN	2	26,201,373 (GRCm38)	missense	probably benign
IGL02691:Lhx3	APN	2	26,203,085 (GRCm38)	missense	probably damaging	1.00
R0267:Lhx3	UTSW	2	26,203,028 (GRCm38)	missense	probably benign	0.02
R0571:Lhx3	UTSW	2	26,201,124 (GRCm38)	missense	probably damaging	1.00
R0574:Lhx3	UTSW	2	26,201,311 (GRCm38)	missense	probably benign	0.00
R1866:Lhx3	UTSW	2	26,203,974 (GRCm38)	missense	probably damaging	0.99
R1926:Lhx3	UTSW	2	26,202,188 (GRCm38)	nonsense	probably null
R1940:Lhx3	UTSW	2	26,203,962 (GRCm38)	missense	probably benign	0.05
R3147:Lhx3	UTSW	2	26,201,265 (GRCm38)	missense	probably benign	0.01
R4389:Lhx3	UTSW	2	26,201,090 (GRCm38)	utr 3 prime	probably benign
R4534:Lhx3	UTSW	2	26,204,014 (GRCm38)	missense	probably benign
R4551:Lhx3	UTSW	2	26,201,190 (GRCm38)	missense	probably damaging	1.00
R4761:Lhx3	UTSW	2	26,201,423 (GRCm38)	frame shift	probably null
R5102:Lhx3	UTSW	2	26,201,423 (GRCm38)	frame shift	probably null
R5105:Lhx3	UTSW	2	26,201,423 (GRCm38)	frame shift	probably null
R5673:Lhx3	UTSW	2	26,202,994 (GRCm38)	missense	probably damaging	1.00
R5751:Lhx3	UTSW	2	26,201,161 (GRCm38)	missense	probably benign
R6180:Lhx3	UTSW	2	26,201,491 (GRCm38)	missense	probably benign
R6262:Lhx3	UTSW	2	26,202,423 (GRCm38)	small deletion	probably benign
R7238:Lhx3	UTSW	2	26,202,997 (GRCm38)	missense	probably damaging	1.00
R8934:Lhx3	UTSW	2	26,202,246 (GRCm38)	missense	probably damaging	0.98
Z1176:Lhx3	UTSW	2	26,203,987 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAAGAAATGGTCACTGGCTTG -3'
(R):5'- AGAGCAGTACCGAGAGCTAC -3'

Sequencing Primer
(F):5'- GACTTTGGAGTCCCTCAGC -3'
(R):5'- TACCGAGAGCTACGCCCAG -3'

Posted On

2016-09-01