Mutagenetix > Incidental Mutation

Incidental Mutation 'R6853:Lhx9'

535069

Institutional Source

Beutler Lab

Gene Symbol

Lhx9

Ensembl Gene

ENSMUSG00000019230

Gene Name

LIM homeobox protein 9

Synonyms

3110009O07Rik, Lhx9 alpha, LH2B

MMRRC Submission

044956-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.787) question?

Stock #

R6853 (G1)

Quality Score

217.468

Status

Validated

Chromosome

Chromosomal Location

138752924-138776315 bp(-) (GRCm39)

Type of Mutation

frame shift

DNA Base Change (assembly)

ACC to ACCC at 138769544 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000142268 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000019374] [ENSMUST00000046870] [ENSMUST00000093486] [ENSMUST00000112026] [ENSMUST00000112030] [ENSMUST00000194557]

AlphaFold

Q9WUH2

Predicted Effect

probably null
Transcript: ENSMUST00000019374

SMART Domains

Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	70	123	4.48e-17	SMART
LIM	132	186	8.04e-19	SMART
HOX	267	319	1.89e-4	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000046870

SMART Domains

Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	61	114	4.48e-17	SMART
LIM	123	177	8.04e-19	SMART
HOX	258	320	8.07e-22	SMART
low complexity region	344	368	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000093486

SMART Domains

Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	61	114	4.48e-17	SMART
LIM	123	177	8.04e-19	SMART
HOX	258	310	1.89e-4	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000112026

SMART Domains

Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	70	123	4.48e-17	SMART
LIM	132	186	8.04e-19	SMART
HOX	267	329	8.07e-22	SMART
low complexity region	353	377	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000112030

SMART Domains

Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	61	114	4.48e-17	SMART
LIM	123	177	8.04e-19	SMART
HOX	258	310	1.89e-4	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000194557

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.0%

Validation Efficiency

98% (63/64)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the LIM homeobox gene family of developmentally expressed transcription factors. The encoded protein contains a homeodomain and two cysteine-rich zinc-binding LIM domains involved in protein-protein interactions. The protein is highly similar to a mouse protein that causes gonadal agenesis when inactivated, suggesting a role in gonadal development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit failed proliferation of the somatic cells of the genital ridge resulting in lack of discrete gonad formation, infertility in both sexes, and female-like genitalia in genetically male mice. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6030458C11Rik	G	T	15: 12,818,031 (GRCm39)	D138E	probably benign	Het
Atp13a5	A	G	16: 29,140,480 (GRCm39)	S359P	possibly damaging	Het
Bcam	T	C	7: 19,494,331 (GRCm39)	D355G	probably damaging	Het
Bmp8a	C	A	4: 123,236,476 (GRCm39)	W9L	unknown	Het
Cacul1	A	T	19: 60,517,904 (GRCm39)	Y334*	probably null	Het
Ccdc178	A	T	18: 22,242,933 (GRCm39)	N227K	probably benign	Het
Ceacam2	T	C	7: 25,217,561 (GRCm39)	N318S	possibly damaging	Het
Cntrl	T	A	2: 35,019,833 (GRCm39)	S553R	possibly damaging	Het
Ctsa	T	A	2: 164,679,284 (GRCm39)	M331K	probably benign	Het
Cyp2c38	T	A	19: 39,426,748 (GRCm39)	Q184H	probably benign	Het
Cyp2c70	C	T	19: 40,172,364 (GRCm39)	E93K	possibly damaging	Het
D430041D05Rik	C	T	2: 104,071,500 (GRCm39)	V1267M	probably damaging	Het
Ddias	C	T	7: 92,508,773 (GRCm39)	A381T	possibly damaging	Het
Dnhd1	G	A	7: 105,352,935 (GRCm39)	C2696Y	probably benign	Het
Efr3a	G	A	15: 65,701,679 (GRCm39)	V198I	probably benign	Het
Farp2	T	C	1: 93,497,738 (GRCm39)	F256S	probably damaging	Het
Fga	A	G	3: 82,938,219 (GRCm39)	Y198C	probably damaging	Het
Gabpa	T	A	16: 84,657,387 (GRCm39)	C421S	probably damaging	Het
Gm21798	A	T	15: 64,689,714 (GRCm39)		probably benign	Het
Gm21798	A	T	15: 64,689,716 (GRCm39)		probably benign	Het
Gm7145	A	C	1: 117,913,874 (GRCm39)	N252T	possibly damaging	Het
H2-Q6	T	C	17: 35,647,335 (GRCm39)	*327R	probably null	Het
H6pd	T	C	4: 150,066,919 (GRCm39)	D489G	probably benign	Het
Htra2	A	G	6: 83,030,812 (GRCm39)		probably benign	Het
Ice1	T	G	13: 70,751,421 (GRCm39)	E1555A	possibly damaging	Het
Inpp5d	T	A	1: 87,609,402 (GRCm39)		probably null	Het
Itih2	T	C	2: 10,120,077 (GRCm39)	D320G	probably damaging	Het
Kif1a	T	G	1: 92,967,524 (GRCm39)	H1129P	possibly damaging	Het
Kmt2a	G	A	9: 44,729,704 (GRCm39)		probably benign	Het
L3mbtl4	G	A	17: 69,084,915 (GRCm39)	D609N	probably damaging	Het
Lgals9	A	T	11: 78,856,832 (GRCm39)	D248E	probably benign	Het
Msh3	A	G	13: 92,449,080 (GRCm39)		probably null	Het
Mtus2	A	G	5: 148,043,821 (GRCm39)	K803R	probably damaging	Het
Oas1a	T	A	5: 121,045,491 (GRCm39)	I17L	possibly damaging	Het
Or2h2c	G	A	17: 37,422,400 (GRCm39)	T158I	probably benign	Het
Or5b121	T	A	19: 13,507,295 (GRCm39)	I130K	possibly damaging	Het
Or5k15	C	T	16: 58,710,121 (GRCm39)	S154N	possibly damaging	Het
Or5k15	T	A	16: 58,710,122 (GRCm39)	S154C	probably damaging	Het
Or7g32	T	G	9: 19,408,102 (GRCm39)	Y19*	probably null	Het
Otof	T	C	5: 30,545,583 (GRCm39)	D539G	probably damaging	Het
Pabpc4	T	C	4: 123,188,536 (GRCm39)	Y382H	possibly damaging	Het
Rag1	T	C	2: 101,472,566 (GRCm39)	T859A	probably damaging	Het
Ralbp1	C	T	17: 66,159,751 (GRCm39)	R504H	possibly damaging	Het
Sdk2	A	G	11: 113,671,755 (GRCm39)	F2131S	probably damaging	Het
Sik1	A	T	17: 32,073,180 (GRCm39)		probably null	Het
Sis	A	G	3: 72,798,759 (GRCm39)	I1763T	possibly damaging	Het
Slc39a6	A	G	18: 24,732,376 (GRCm39)	I304T	possibly damaging	Het
Slc5a12	A	G	2: 110,454,539 (GRCm39)	S367G	probably benign	Het
Smchd1	A	T	17: 71,743,738 (GRCm39)	W476R	probably damaging	Het
Spag17	T	C	3: 99,920,551 (GRCm39)	Y429H	possibly damaging	Het
Stt3a	G	A	9: 36,653,023 (GRCm39)	S553F	possibly damaging	Het
Sult2a1	C	T	7: 13,535,412 (GRCm39)	V214I	possibly damaging	Het
Supt6	T	C	11: 78,123,656 (GRCm39)	E38G	possibly damaging	Het
Tenm4	G	A	7: 96,486,502 (GRCm39)	G990R	possibly damaging	Het
Thop1	T	C	10: 80,911,495 (GRCm39)		probably null	Het
Thumpd2	C	A	17: 81,372,459 (GRCm39)	D11Y	possibly damaging	Het
Tmf1	T	G	6: 97,145,810 (GRCm39)	I574L	probably damaging	Het
Tnfaip3	A	G	10: 18,879,499 (GRCm39)	V623A	probably benign	Het
Ttll3	CAAAGTAA	CAAAGTAAAGTAA	6: 113,376,118 (GRCm39)		probably null	Het
Ush2a	T	G	1: 188,643,434 (GRCm39)	Y4265*	probably null	Het
Vamp5	G	A	6: 72,357,424 (GRCm39)		probably benign	Het
Vmn2r12	A	T	5: 109,240,771 (GRCm39)	L114Q	probably damaging	Het
Vmn2r98	A	T	17: 19,286,063 (GRCm39)	Y187F	probably benign	Het

Other mutations in Lhx9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00955:Lhx9	APN	1	138,756,418 (GRCm39)	missense	possibly damaging	0.74
IGL01624:Lhx9	APN	1	138,760,521 (GRCm39)	nonsense	probably null
IGL02149:Lhx9	APN	1	138,759,172 (GRCm39)	missense	probably damaging	1.00
IGL02452:Lhx9	APN	1	138,769,580 (GRCm39)	missense	probably damaging	1.00
IGL02982:Lhx9	APN	1	138,766,349 (GRCm39)	missense	probably damaging	1.00
R0123:Lhx9	UTSW	1	138,766,417 (GRCm39)	missense	probably damaging	1.00
R0134:Lhx9	UTSW	1	138,766,417 (GRCm39)	missense	probably damaging	1.00
R0141:Lhx9	UTSW	1	138,767,744 (GRCm39)	missense	possibly damaging	0.86
R0225:Lhx9	UTSW	1	138,766,417 (GRCm39)	missense	probably damaging	1.00
R0281:Lhx9	UTSW	1	138,760,642 (GRCm39)	missense	probably benign	0.00
R1460:Lhx9	UTSW	1	138,766,447 (GRCm39)	splice site	probably benign
R1932:Lhx9	UTSW	1	138,769,747 (GRCm39)	start gained	probably benign
R4738:Lhx9	UTSW	1	138,760,486 (GRCm39)	missense	probably damaging	1.00
R4792:Lhx9	UTSW	1	138,766,089 (GRCm39)	missense	possibly damaging	0.87
R4820:Lhx9	UTSW	1	138,766,105 (GRCm39)	missense	probably benign	0.00
R4877:Lhx9	UTSW	1	138,766,092 (GRCm39)	missense	probably benign	0.04
R6035:Lhx9	UTSW	1	138,766,281 (GRCm39)	missense	possibly damaging	0.67
R6035:Lhx9	UTSW	1	138,766,281 (GRCm39)	missense	possibly damaging	0.67
R6825:Lhx9	UTSW	1	138,769,544 (GRCm39)	frame shift	probably null
R6852:Lhx9	UTSW	1	138,769,544 (GRCm39)	frame shift	probably null
R7264:Lhx9	UTSW	1	138,760,489 (GRCm39)	missense	probably damaging	0.98
R8097:Lhx9	UTSW	1	138,766,089 (GRCm39)	missense	probably damaging	0.97
R8164:Lhx9	UTSW	1	138,760,518 (GRCm39)	missense	probably damaging	1.00
R8245:Lhx9	UTSW	1	138,766,179 (GRCm39)	missense	probably benign	0.24
R8278:Lhx9	UTSW	1	138,766,324 (GRCm39)	missense	probably damaging	0.98
R8951:Lhx9	UTSW	1	138,769,704 (GRCm39)	missense	probably damaging	1.00
R9761:Lhx9	UTSW	1	138,774,934 (GRCm39)	missense	probably benign	0.09
Z1177:Lhx9	UTSW	1	138,759,236 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CTGGAGAGCTCAGGACTACAAC -3'
(R):5'- CTTCACTCGAATGAACTGAGAGC -3'

Sequencing Primer
(F):5'- ACATCTTAGACACCTCGATTCGG -3'
(R):5'- TCGAATGAACTGAGAGCCCCAG -3'

Posted On

2018-09-12