Mutagenetix > Incidental Mutation

Incidental Mutation 'R5475:Ldb2'

434010

Institutional Source

Beutler Lab

Gene Symbol

Ldb2

Ensembl Gene

ENSMUSG00000039706

Gene Name

LIM domain binding 2

Synonyms

CLIM1, Ldb3, CLIM-1a, CLIM-1b, CLP-36

MMRRC Submission

043036-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5475 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

44629474-44957022 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 44699174 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 88 (Y88C)

Ref Sequence

ENSEMBL: ENSMUSP00000142442 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070748] [ENSMUST00000199256] [ENSMUST00000199261] [ENSMUST00000199534]

AlphaFold

O55203

Predicted Effect

probably damaging
Transcript: ENSMUST00000070748
AA Change: Y88C

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

SMART Domains

Protein: ENSMUSP00000067737
Gene: ENSMUSG00000039706
AA Change: Y88C

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	30	232	9.9e-56	PFAM
low complexity region	249	281	N/A	INTRINSIC
PDB:2JTN\|A	293	337	2e-21	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000198894

Predicted Effect

probably damaging
Transcript: ENSMUST00000199256
AA Change: Y88C

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

SMART Domains

Protein: ENSMUSP00000143775
Gene: ENSMUSG00000039706
AA Change: Y88C

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	30	232	6.9e-56	PFAM
low complexity region	249	281	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000199261
AA Change: Y88C

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

SMART Domains

Protein: ENSMUSP00000143289
Gene: ENSMUSG00000039706
AA Change: Y88C

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	29	233	2.3e-68	PFAM
low complexity region	249	281	N/A	INTRINSIC
PDB:2YPA\|D	296	335	2e-20	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199471

Predicted Effect

probably damaging
Transcript: ENSMUST00000199534
AA Change: Y88C

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

SMART Domains

Protein: ENSMUSP00000142442
Gene: ENSMUSG00000039706
AA Change: Y88C

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	29	233	2e-71	PFAM
low complexity region	249	281	N/A	INTRINSIC

Meta Mutation Damage Score

0.9587

Coding Region Coverage

1x: 98.3%
3x: 97.4%
10x: 95.5%
20x: 91.8%

Validation Efficiency

96% (72/75)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the LIM-domain binding family. Members of this family are characterized by a conserved nuclear localization sequence, an amino-terminal homodimerization domain and a carboxy-terminal LIM interaction domain. These proteins function as adapter molecules to allow assembly of transcriptional regulatory complexes. Genetic association studies suggest functions for this gene in rhegmatogenous retinal detachment and coronary artery disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
PHENOTYPE: Homozygous mutation of this gene results in no obvious phenotype. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930505A04Rik	C	T	11: 30,376,349 (GRCm39)	V173M	probably damaging	Het
AA467197	A	G	2: 122,482,646 (GRCm39)	K70R	probably damaging	Het
Agr3	A	G	12: 35,997,539 (GRCm39)	N83S	probably benign	Het
Alpk2	T	C	18: 65,440,083 (GRCm39)	T904A	probably benign	Het
Ank	A	T	15: 27,557,285 (GRCm39)	K156N	probably damaging	Het
Arsb	T	G	13: 93,998,773 (GRCm39)	D360E	probably benign	Het
Atg14	C	T	14: 47,805,793 (GRCm39)	R24Q	possibly damaging	Het
Cacna1e	A	T	1: 154,601,455 (GRCm39)	F71I	possibly damaging	Het
Cdc42bpg	T	C	19: 6,361,101 (GRCm39)	I242T	probably damaging	Het
Cngb1	A	T	8: 95,978,597 (GRCm39)	I588N	probably damaging	Het
Col6a6	T	C	9: 105,651,537 (GRCm39)	H1158R	probably null	Het
Cse1l	T	C	2: 166,783,174 (GRCm39)	S684P	probably damaging	Het
Cyp2c29	A	T	19: 39,318,731 (GRCm39)	M404L	possibly damaging	Het
D5Ertd579e	G	T	5: 36,772,601 (GRCm39)	S598Y	probably damaging	Het
Dph7	A	T	2: 24,858,969 (GRCm39)		probably null	Het
Dsg1c	A	T	18: 20,415,088 (GRCm39)	N662Y	probably damaging	Het
Efcab9	T	G	11: 32,472,862 (GRCm39)	D195A	probably damaging	Het
Ephb4	A	G	5: 137,352,701 (GRCm39)	M95V	probably benign	Het
Fam171a1	A	T	2: 3,226,334 (GRCm39)	Y489F	possibly damaging	Het
Fars2	T	C	13: 36,388,553 (GRCm39)	I14T	probably benign	Het
Fbxo34	T	C	14: 47,766,802 (GRCm39)	V54A	probably benign	Het
Fbxw17	T	C	13: 50,579,684 (GRCm39)	I167T	probably benign	Het
Fzd9	A	T	5: 135,279,123 (GRCm39)		probably null	Het
Gm26996	T	A	6: 130,556,918 (GRCm39)		noncoding transcript	Het
Gm4744	A	G	6: 40,927,388 (GRCm39)		probably benign	Het
Gm4744	T	A	6: 40,927,403 (GRCm39)		probably benign	Het
Gprc5c	G	T	11: 114,755,093 (GRCm39)	V257L	possibly damaging	Het
Has1	C	A	17: 18,068,583 (GRCm39)	R257L	possibly damaging	Het
Hjv	T	C	3: 96,434,599 (GRCm39)	S113P	probably benign	Het
Hsd17b8	C	T	17: 34,246,287 (GRCm39)		probably benign	Het
Kat2b	T	G	17: 53,970,609 (GRCm39)	V665G	probably damaging	Het
Klhdc4	T	A	8: 122,526,311 (GRCm39)	H276L	possibly damaging	Het
Klhl6	A	T	16: 19,766,877 (GRCm39)	C506S	probably damaging	Het
Lrit1	A	G	14: 36,776,958 (GRCm39)	E26G	probably benign	Het
Mcoln2	A	G	3: 145,889,541 (GRCm39)	Y414C	probably damaging	Het
Mfsd5	A	G	15: 102,188,928 (GRCm39)	D100G	probably damaging	Het
Micall2	T	A	5: 139,702,224 (GRCm39)	S340C	probably damaging	Het
Npsr1	T	C	9: 24,211,715 (GRCm39)	I81T	probably damaging	Het
Or2bd2	G	T	7: 6,443,169 (GRCm39)	R90L	probably benign	Het
Or2t49	A	G	11: 58,392,431 (GRCm39)	V317A	probably benign	Het
Or6x1	T	A	9: 40,099,005 (GRCm39)	L198H	possibly damaging	Het
Or8b56	T	A	9: 38,739,762 (GRCm39)	F258L	possibly damaging	Het
Pax3	T	C	1: 78,080,055 (GRCm39)	T444A	probably benign	Het
Pea15a	A	G	1: 172,026,809 (GRCm39)		probably null	Het
Phc1	T	A	6: 122,311,051 (GRCm39)	Q95L	possibly damaging	Het
Plch2	T	C	4: 155,084,594 (GRCm39)	Y361C	probably damaging	Het
Pphln1-ps1	A	T	16: 13,494,977 (GRCm39)	R25S	possibly damaging	Het
Rad54l2	C	T	9: 106,583,057 (GRCm39)	G787D	probably damaging	Het
Rbm20	G	T	19: 53,823,136 (GRCm39)	E578*	probably null	Het
Sipa1l2	A	T	8: 126,218,334 (GRCm39)	D334E	probably damaging	Het
Tbc1d2	C	T	4: 46,629,912 (GRCm39)	G252R	probably benign	Het
Thumpd1	A	G	7: 119,319,943 (GRCm39)	S8P	probably benign	Het
Tnxb	T	C	17: 34,908,567 (GRCm39)	Y1407H	probably damaging	Het
Trav2	T	A	14: 52,805,290 (GRCm39)	V37E	probably damaging	Het
Trav3-1	G	T	14: 52,818,494 (GRCm39)	W56L	probably damaging	Het
Usp31	A	T	7: 121,250,749 (GRCm39)	L808Q	probably damaging	Het
Vmn1r52	C	T	6: 90,155,894 (GRCm39)	A66V	probably benign	Het
Vmn2r105	T	A	17: 20,455,044 (GRCm39)	I31L	probably benign	Het
Wdr1	C	T	5: 38,686,931 (GRCm39)	G278S	probably damaging	Het
Zbtb2	G	T	10: 4,319,275 (GRCm39)	F250L	probably benign	Het

Other mutations in Ldb2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00504:Ldb2	APN	5	44,699,026 (GRCm39)	splice site	probably null
IGL01757:Ldb2	APN	5	44,699,209 (GRCm39)	splice site	probably benign
IGL01936:Ldb2	APN	5	44,637,586 (GRCm39)	missense	probably damaging	1.00
IGL03105:Ldb2	APN	5	44,956,715 (GRCm39)	missense	possibly damaging	0.70
IGL03108:Ldb2	APN	5	44,699,057 (GRCm39)	missense	probably damaging	1.00
R0152:Ldb2	UTSW	5	44,699,141 (GRCm39)	missense	possibly damaging	0.86
R0178:Ldb2	UTSW	5	44,630,841 (GRCm39)	missense	probably damaging	1.00
R0841:Ldb2	UTSW	5	44,690,016 (GRCm39)	missense	probably damaging	1.00
R1145:Ldb2	UTSW	5	44,690,016 (GRCm39)	missense	probably damaging	1.00
R1145:Ldb2	UTSW	5	44,690,016 (GRCm39)	missense	probably damaging	1.00
R1318:Ldb2	UTSW	5	44,692,379 (GRCm39)	critical splice donor site	probably null
R1607:Ldb2	UTSW	5	44,630,814 (GRCm39)	missense	probably damaging	0.99
R2863:Ldb2	UTSW	5	44,637,666 (GRCm39)	missense	probably damaging	0.99
R3803:Ldb2	UTSW	5	44,630,736 (GRCm39)	missense	probably benign	0.38
R4502:Ldb2	UTSW	5	44,826,749 (GRCm39)	missense	probably damaging	1.00
R4613:Ldb2	UTSW	5	44,633,893 (GRCm39)	missense	probably benign	0.27
R4985:Ldb2	UTSW	5	44,637,645 (GRCm39)	missense	probably damaging	1.00
R5512:Ldb2	UTSW	5	44,637,586 (GRCm39)	missense	probably damaging	1.00
R6058:Ldb2	UTSW	5	44,633,905 (GRCm39)	missense	possibly damaging	0.66
R6282:Ldb2	UTSW	5	44,690,007 (GRCm39)	missense	probably damaging	1.00
R6438:Ldb2	UTSW	5	44,637,652 (GRCm39)	missense	probably damaging	0.98
R6770:Ldb2	UTSW	5	44,826,738 (GRCm39)	missense	probably damaging	0.99
R6830:Ldb2	UTSW	5	44,699,199 (GRCm39)	missense	probably damaging	1.00
R8061:Ldb2	UTSW	5	44,637,612 (GRCm39)	missense	probably damaging	1.00
R8819:Ldb2	UTSW	5	44,956,757 (GRCm39)	nonsense	probably null
R8820:Ldb2	UTSW	5	44,956,757 (GRCm39)	nonsense	probably null
X0026:Ldb2	UTSW	5	44,690,070 (GRCm39)	missense	probably damaging	0.99
X0028:Ldb2	UTSW	5	44,699,136 (GRCm39)	missense	probably benign	0.04

Predicted Primers

PCR Primer
(F):5'- TTAAGGATGTAGCTATAGGCAAGCC -3'
(R):5'- AAACCTCCGTGAGATGGTG -3'

Sequencing Primer
(F):5'- AGGCAAGCCTATTCCATACCTTGG -3'
(R):5'- GGTCCCATTTTTCCCAAATAGTTAGG -3'

Posted On

2016-10-06