Mutagenetix > Incidental Mutation

Incidental Mutation 'R1585:Ldb1'

177479

Institutional Source

Beutler Lab

Gene Symbol

Ldb1

Ensembl Gene

ENSMUSG00000025223

Gene Name

LIM domain binding 1

Synonyms

CLIM2

MMRRC Submission

039622-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1585 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

46020009-46033653 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 46022903 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 261 (T261A)

Ref Sequence

ENSEMBL: ENSMUSP00000139562 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026252] [ENSMUST00000056931] [ENSMUST00000137771] [ENSMUST00000152946] [ENSMUST00000156585] [ENSMUST00000185355]

AlphaFold

P70662

Predicted Effect

probably damaging
Transcript: ENSMUST00000026252
AA Change: T225A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000026252
Gene: ENSMUSG00000025223
AA Change: T225A

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	32	236	1e-72	PFAM
low complexity region	264	287	N/A	INTRINSIC
PDB:2JTN\|A	295	339	1e-22	PDB
low complexity region	355	368	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000056931
AA Change: T225A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000053680
Gene: ENSMUSG00000025223
AA Change: T225A

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	32	236	1e-72	PFAM
low complexity region	264	287	N/A	INTRINSIC
PDB:2JTN\|A	295	339	1e-22	PDB
low complexity region	355	368	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126320

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136203

Predicted Effect

possibly damaging
Transcript: ENSMUST00000137771
AA Change: T225A

PolyPhen 2 Score 0.851 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000114667
Gene: ENSMUSG00000025223
AA Change: T225A

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	32	236	5.4e-73	PFAM
low complexity region	264	287	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000152946
AA Change: T225A

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000116909
Gene: ENSMUSG00000025223
AA Change: T225A

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	33	189	1.1e-42	PFAM
Pfam:LIM_bind	178	235	5.5e-15	PFAM
low complexity region	264	287	N/A	INTRINSIC
PDB:2YPA\|D	298	337	4e-21	PDB
low complexity region	353	366	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000156585
AA Change: T261A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000118546
Gene: ENSMUSG00000025223
AA Change: T261A

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	69	225	5.9e-42	PFAM
Pfam:LIM_bind	214	271	2.5e-14	PFAM
low complexity region	300	323	N/A	INTRINSIC
PDB:2JTN\|A	331	375	2e-22	PDB
low complexity region	391	404	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000185355
AA Change: T261A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139562
Gene: ENSMUSG00000025223
AA Change: T261A

Domain	Start	End	E-Value	Type
Pfam:LIM_bind	68	272	5.6e-73	PFAM
low complexity region	300	323	N/A	INTRINSIC
PDB:2JTN\|A	331	375	2e-22	PDB
low complexity region	391	404	N/A	INTRINSIC

Meta Mutation Damage Score

0.1285

Coding Region Coverage

1x: 99.1%
3x: 98.1%
10x: 95.7%
20x: 91.2%

Validation Efficiency

95% (81/85)

MGI Phenotype

PHENOTYPE: Mice homozygous for disruptions in this gene die as embryos at E9.5-E10 with impaired primitive erythropoiesis and vascular development. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310057J18Rik	T	A	10: 28,858,518 (GRCm39)	I50F	possibly damaging	Het
4930505A04Rik	T	C	11: 30,377,175 (GRCm39)		probably benign	Het
Aadat	A	T	8: 60,979,714 (GRCm39)	D192V	possibly damaging	Het
Akap12	A	G	10: 4,303,640 (GRCm39)	D150G	probably benign	Het
Amigo3	A	T	9: 107,931,231 (GRCm39)	N218I	probably damaging	Het
Ankmy1	A	G	1: 92,827,373 (GRCm39)	S60P	probably benign	Het
Apol7e	G	A	15: 77,602,029 (GRCm39)	S209N	probably damaging	Het
AW551984	A	T	9: 39,510,632 (GRCm39)	Y234*	probably null	Het
Bcam	A	T	7: 19,494,111 (GRCm39)	D393E	probably damaging	Het
Card9	A	G	2: 26,244,398 (GRCm39)	L444P	probably benign	Het
Ccar1	T	C	10: 62,586,780 (GRCm39)	E886G	unknown	Het
Ccnb2	A	T	9: 70,317,559 (GRCm39)		probably null	Het
Cd276	T	C	9: 58,442,838 (GRCm39)	S206G	probably damaging	Het
Cds1	T	A	5: 101,965,828 (GRCm39)		probably benign	Het
Cfap96	G	A	8: 46,409,515 (GRCm39)	S268L	probably benign	Het
Chuk	T	C	19: 44,065,812 (GRCm39)	S661G	possibly damaging	Het
Col17a1	T	C	19: 47,639,276 (GRCm39)	N1090D	probably benign	Het
Col3a1	A	T	1: 45,367,026 (GRCm39)		probably null	Het
Crispld1	G	T	1: 17,821,024 (GRCm39)	V355F	possibly damaging	Het
Cspg4	A	T	9: 56,806,151 (GRCm39)	R2321W	probably damaging	Het
Dner	T	C	1: 84,563,177 (GRCm39)	T61A	probably benign	Het
Dnmt3a	A	T	12: 3,951,660 (GRCm39)	Y679F	probably damaging	Het
Dzip3	A	T	16: 48,798,241 (GRCm39)		probably benign	Het
Eif3l	T	C	15: 78,968,381 (GRCm39)	S217P	possibly damaging	Het
Fbxo42	T	A	4: 140,925,417 (GRCm39)		probably benign	Het
Fhod1	A	T	8: 106,063,957 (GRCm39)		probably benign	Het
Fzd1	T	A	5: 4,806,278 (GRCm39)	I435F	probably damaging	Het
Gapvd1	C	T	2: 34,602,207 (GRCm39)	V647I	possibly damaging	Het
Gm14496	T	C	2: 181,638,002 (GRCm39)	S359P	possibly damaging	Het
Gm5218	C	A	15: 81,383,741 (GRCm39)		noncoding transcript	Het
Hnrnph3	A	G	10: 62,851,579 (GRCm39)		probably null	Het
Hsd17b12	G	T	2: 93,864,321 (GRCm39)	T262K	probably damaging	Het
Igsf10	G	C	3: 59,237,838 (GRCm39)	P781R	probably damaging	Het
Il11ra1	T	A	4: 41,768,207 (GRCm39)	S373T	probably damaging	Het
Kdm3b	A	G	18: 34,942,345 (GRCm39)	D612G	probably damaging	Het
Lep	C	A	6: 29,069,089 (GRCm39)	H47N	possibly damaging	Het
Lrrtm2	A	T	18: 35,346,428 (GRCm39)	S291R	possibly damaging	Het
Ncor2	T	C	5: 125,162,062 (GRCm39)	Q404R	unknown	Het
Nlrp4d	T	C	7: 10,116,437 (GRCm39)	H148R	probably benign	Het
Nlrp9a	T	A	7: 26,258,093 (GRCm39)	D570E	probably benign	Het
Nphp3	G	A	9: 103,886,413 (GRCm39)	V202I	probably damaging	Het
Nptn	T	A	9: 58,548,073 (GRCm39)	N159K	probably benign	Het
Or4a69	T	A	2: 89,313,315 (GRCm39)	T55S	probably benign	Het
Or4a72	A	T	2: 89,405,746 (GRCm39)	V108D	possibly damaging	Het
Or51f2	G	A	7: 102,526,980 (GRCm39)	V218I	probably benign	Het
Or52a24	A	T	7: 103,381,585 (GRCm39)	T151S	possibly damaging	Het
Or8b53	A	T	9: 38,667,716 (GRCm39)	H244L	probably damaging	Het
Pcolce	T	A	5: 137,608,769 (GRCm39)	R13*	probably null	Het
Pdgfra	A	G	5: 75,353,264 (GRCm39)	Y1018C	probably damaging	Het
Prima1	A	G	12: 103,201,854 (GRCm39)	S74P	probably damaging	Het
Prl7c1	A	G	13: 27,962,838 (GRCm39)	L55P	probably damaging	Het
Rasef	A	G	4: 73,658,574 (GRCm39)	V513A	probably damaging	Het
Rgs1	T	C	1: 144,121,227 (GRCm39)		probably null	Het
Rlf	T	C	4: 121,005,488 (GRCm39)	E1164G	probably benign	Het
Rnf213	A	T	11: 119,354,171 (GRCm39)	N4016I	probably damaging	Het
Sae1	C	T	7: 16,064,537 (GRCm39)		probably null	Het
Serping1	A	T	2: 84,601,848 (GRCm39)	D207E	probably benign	Het
Setd2	T	A	9: 110,380,464 (GRCm39)	D33E	unknown	Het
Simc1	T	C	13: 54,673,071 (GRCm39)	M473T	probably benign	Het
Slc30a6	T	A	17: 74,725,610 (GRCm39)		probably benign	Het
Slc4a5	T	C	6: 83,242,669 (GRCm39)	L346P	probably damaging	Het
Spef2	T	A	15: 9,596,660 (GRCm39)	Q1473L	probably damaging	Het
St3gal3	G	T	4: 117,817,204 (GRCm39)	A44D	possibly damaging	Het
Sv2b	G	T	7: 74,797,425 (GRCm39)	T323K	probably damaging	Het
Sycp2	T	A	2: 177,993,461 (GRCm39)	N1228I	possibly damaging	Het
Thbs2	T	A	17: 14,910,030 (GRCm39)	M190L	probably benign	Het
Tnrc6a	G	A	7: 122,776,098 (GRCm39)	V1190I	probably benign	Het
Utrn	A	T	10: 12,312,029 (GRCm39)	I673K	possibly damaging	Het
Vmn2r114	C	T	17: 23,510,675 (GRCm39)	V602M	probably damaging	Het
Wdr7	A	T	18: 64,057,989 (GRCm39)	I1273L	probably benign	Het
Zfp618	T	C	4: 63,051,175 (GRCm39)	L652P	probably damaging	Het
Zfp804a	G	A	2: 81,884,095 (GRCm39)		probably benign	Het

Other mutations in Ldb1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01603:Ldb1	APN	19	46,024,014 (GRCm39)	missense	probably damaging	1.00
IGL02069:Ldb1	APN	19	46,021,617 (GRCm39)	missense	possibly damaging	0.88
IGL02380:Ldb1	APN	19	46,022,929 (GRCm39)	missense	possibly damaging	0.95
IGL02441:Ldb1	APN	19	46,024,195 (GRCm39)	missense	probably damaging	0.99
IGL02677:Ldb1	APN	19	46,024,594 (GRCm39)	splice site	probably benign
R3720:Ldb1	UTSW	19	46,033,331 (GRCm39)	start gained	probably benign
R4897:Ldb1	UTSW	19	46,023,132 (GRCm39)	missense	probably benign
R5830:Ldb1	UTSW	19	46,022,557 (GRCm39)	missense	probably benign	0.00
R7663:Ldb1	UTSW	19	46,023,963 (GRCm39)	missense	probably damaging	1.00
R8482:Ldb1	UTSW	19	46,024,709 (GRCm39)	missense	probably null	0.99
R8887:Ldb1	UTSW	19	46,023,294 (GRCm39)	missense	probably damaging	1.00
R9742:Ldb1	UTSW	19	46,023,858 (GRCm39)	critical splice donor site	probably null
X0027:Ldb1	UTSW	19	46,022,528 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TCAGCCTTGTAGTCCCAGAAGTGAG -3'
(R):5'- TCAGATGACCTGATACCACTGCCC -3'

Sequencing Primer
(F):5'- CTTGTAGTCCCAGAAGTGAGAAAGG -3'
(R):5'- GTCCAAAAACATTACCCGGTGTG -3'

Posted On

2014-04-24