Mutagenetix > Incidental Mutations

Incidental Mutation 'IGL02452:Lhx9'

293704

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Lhx9

Ensembl Gene

ENSMUSG00000019230

Gene Name

LIM homeobox protein 9

Synonyms

3110009O07Rik, Lhx9 alpha, LH2B

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.784) question?

Stock #

IGL02452

Quality Score

Status

Chromosome

Chromosomal Location

138825186-138848577 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 138841842 bp

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 47 (L47Q)

Ref Sequence

ENSEMBL: ENSMUSP00000142268 (fasta)

Gene Model

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000019374
AA Change: L47Q

PolyPhen 2 Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: L47Q

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 damaging
Transcript: ENSMUST00000046870
AA Change: L38Q

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: L38Q

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 damaging
Transcript: ENSMUST00000093486
AA Change: L38Q

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: L38Q

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

possibly damaging
Transcript: ENSMUST00000112026
AA Change: L47Q

PolyPhen 2 Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: L47Q

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 damaging
Transcript: ENSMUST00000112030
AA Change: L38Q

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: L38Q

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 damaging
Transcript: ENSMUST00000194557
AA Change: L47Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Coding Region Coverage

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 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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acadm	C	A	3: 153,941,970	V11F	probably damaging	Het
Alk	A	T	17: 71,902,625	Y941*	probably null	Het
Armc4	C	T	18: 7,129,461	E906K	probably damaging	Het
Blm	A	T	7: 80,503,377		probably null	Het
Blvrb	T	C	7: 27,459,340	V55A	possibly damaging	Het
Cdh23	T	A	10: 60,317,942	T2288S	probably damaging	Het
Csnk1g1	T	A	9: 66,007,785	M242K	probably damaging	Het
Cyp2c29	G	A	19: 39,290,847	G96D	possibly damaging	Het
Cyp2d26	T	A	15: 82,792,626	H173L	probably benign	Het
Cyp2g1	T	A	7: 26,811,446	S131T	probably benign	Het
Dupd1	G	A	14: 21,702,922	T52I	probably damaging	Het
Dzip3	T	A	16: 48,938,537		probably benign	Het
Espl1	T	C	15: 102,299,839	S427P	probably damaging	Het
Fasn	A	T	11: 120,808,180	D2424E	probably benign	Het
Flrt2	G	A	12: 95,779,483	M198I	probably benign	Het
Gen1	A	T	12: 11,242,575	S404R	probably benign	Het
Gm11596	A	T	11: 99,792,980	C105S	unknown	Het
Gm8765	A	T	13: 50,703,077	H917L	probably damaging	Het
Hdlbp	A	T	1: 93,417,511	V714D	probably damaging	Het
Igkv4-80	A	G	6: 69,016,832	V25A	probably benign	Het
Igkv8-27	C	T	6: 70,171,941	W76*	probably null	Het
Ikzf1	T	C	11: 11,748,545	L132P	probably damaging	Het
Kcna6	C	A	6: 126,738,480	C482F	possibly damaging	Het
Lrp4	T	A	2: 91,474,002	D175E	probably damaging	Het
Lrrtm3	T	C	10: 64,088,036	K451E	probably damaging	Het
Mcm9	C	T	10: 53,541,557	V17M	probably damaging	Het
Mios	T	A	6: 8,222,492	S475R	probably benign	Het
Mmp24	C	T	2: 155,815,788	R533C	probably damaging	Het
Moxd1	C	T	10: 24,282,752	P435S	probably damaging	Het
Mta2	T	A	19: 8,950,306	I497N	probably benign	Het
Mtus2	T	C	5: 148,077,663	V422A	probably benign	Het
Ndufaf1	A	T	2: 119,656,426	F260Y	probably damaging	Het
Nfasc	C	T	1: 132,620,924		probably null	Het
Nid1	A	T	13: 13,508,720	T1128S	probably benign	Het
Olfr583	A	G	7: 103,051,931	D211G	probably benign	Het
Pcdh12	G	A	18: 38,281,693	P793L	probably benign	Het
Pclo	A	T	5: 14,676,966		probably benign	Het
Prpf31	T	A	7: 3,634,186	N161K	possibly damaging	Het
Prpf6	T	G	2: 181,649,085	N656K	probably benign	Het
Ptprn	T	A	1: 75,258,169	H258L	probably benign	Het
Rab19	A	G	6: 39,389,798	T216A	probably benign	Het
Ryr3	A	C	2: 112,833,990	L1652W	probably damaging	Het
Six2	A	C	17: 85,685,378	S232R	possibly damaging	Het
Spag17	T	C	3: 100,027,391	V663A	probably benign	Het
Spag5	A	G	11: 78,304,623	N252S	probably benign	Het
Sptb	C	T	12: 76,609,036		probably null	Het
Synj1	A	G	16: 90,961,365		probably benign	Het
Tekt2	T	C	4: 126,324,852	H36R	possibly damaging	Het
Tjp1	A	T	7: 65,312,655	M1258K	probably damaging	Het
Txnrd3	T	C	6: 89,674,795	*502Q	probably null	Het

Other mutations in Lhx9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00955:Lhx9	APN	1	138828680	missense	possibly damaging	0.74
IGL01624:Lhx9	APN	1	138832783	nonsense	probably null
IGL02149:Lhx9	APN	1	138831434	missense	probably damaging	1.00
IGL02982:Lhx9	APN	1	138838611	missense	probably damaging	1.00
R0123:Lhx9	UTSW	1	138838679	missense	probably damaging	1.00
R0134:Lhx9	UTSW	1	138838679	missense	probably damaging	1.00
R0141:Lhx9	UTSW	1	138840006	missense	possibly damaging	0.86
R0225:Lhx9	UTSW	1	138838679	missense	probably damaging	1.00
R0281:Lhx9	UTSW	1	138832904	missense	probably benign	0.00
R1460:Lhx9	UTSW	1	138838709	splice site	probably benign
R1932:Lhx9	UTSW	1	138842009	start gained	probably benign
R4738:Lhx9	UTSW	1	138832748	missense	probably damaging	1.00
R4792:Lhx9	UTSW	1	138838351	missense	possibly damaging	0.87
R4820:Lhx9	UTSW	1	138838367	missense	probably benign	0.00
R4877:Lhx9	UTSW	1	138838354	missense	probably benign	0.04
R6035:Lhx9	UTSW	1	138838543	missense	possibly damaging	0.67
R6035:Lhx9	UTSW	1	138838543	missense	possibly damaging	0.67
R6825:Lhx9	UTSW	1	138841806	frame shift	probably null
R6852:Lhx9	UTSW	1	138841806	frame shift	probably null
R6853:Lhx9	UTSW	1	138841806	frame shift	probably null
R7264:Lhx9	UTSW	1	138832751	missense	probably damaging	0.98
R8097:Lhx9	UTSW	1	138838351	missense	probably damaging	0.97
R8164:Lhx9	UTSW	1	138832780	missense	probably damaging	1.00
R8245:Lhx9	UTSW	1	138838441	missense	probably benign	0.24
R8278:Lhx9	UTSW	1	138838586	missense	probably damaging	0.98
Z1177:Lhx9	UTSW	1	138831498	missense	probably damaging	0.99

Posted On

2015-04-16