Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01603:Ldb1'

92226

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Ldb1

Ensembl Gene

ENSMUSG00000025223

Gene Name

LIM domain binding 1

Synonyms

CLIM2

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL01603

Quality Score

Status

Chromosome

Chromosomal Location

46020009-46033653 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 46024014 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Lysine at position 124 (I124K)

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: I88K

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000026252
Gene: ENSMUSG00000025223
AA Change: I88K

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: I88K

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000053680
Gene: ENSMUSG00000025223
AA Change: I88K

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: I88K

PolyPhen 2 Score 0.934 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000114667
Gene: ENSMUSG00000025223
AA Change: I88K

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: I88K

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000116909
Gene: ENSMUSG00000025223
AA Change: I88K

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: I124K

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000118546
Gene: ENSMUSG00000025223
AA Change: I124K

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: I124K

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000139562
Gene: ENSMUSG00000025223
AA Change: I124K

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

Coding Region Coverage

Validation Efficiency

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akap8l	T	A	17: 32,564,327 (GRCm39)	D20V	probably damaging	Het
Akr1c12	A	G	13: 4,322,926 (GRCm39)		probably null	Het
Baiap2l1	C	T	5: 144,217,625 (GRCm39)		probably benign	Het
Baz2a	T	C	10: 127,947,037 (GRCm39)	F184L	probably damaging	Het
Cadps	T	C	14: 12,454,154 (GRCm38)		probably benign	Het
Cbr4	A	T	8: 61,956,245 (GRCm39)	*237Y	probably null	Het
Cln3	T	G	7: 126,174,526 (GRCm39)	N275T	probably benign	Het
Csf1r	A	G	18: 61,262,373 (GRCm39)	E823G	probably damaging	Het
Ctr9	C	A	7: 110,648,538 (GRCm39)	A726D	probably damaging	Het
Def6	C	T	17: 28,438,714 (GRCm39)		probably benign	Het
Dock4	T	A	12: 40,743,030 (GRCm39)	I395N	probably damaging	Het
Eln	T	C	5: 134,747,894 (GRCm39)		probably benign	Het
Fasn	A	T	11: 120,706,891 (GRCm39)	H920Q	probably damaging	Het
Glb1l3	A	G	9: 26,770,832 (GRCm39)	I78T	probably damaging	Het
Gm7275	A	T	16: 47,893,942 (GRCm39)		noncoding transcript	Het
Grm5	A	C	7: 87,252,386 (GRCm39)	Y212S	probably damaging	Het
Gtf2ird2	T	C	5: 134,231,129 (GRCm39)		probably benign	Het
Gucy1b1	A	G	3: 81,942,175 (GRCm39)	V528A	probably damaging	Het
Hspg2	G	A	4: 137,280,114 (GRCm39)	A3168T	probably damaging	Het
Kcnj6	A	G	16: 94,634,058 (GRCm39)	S18P	probably benign	Het
Kcnq5	T	A	1: 21,575,564 (GRCm39)	K294I	possibly damaging	Het
Lama4	G	A	10: 38,941,642 (GRCm39)	G693E	possibly damaging	Het
Lrrfip1	C	T	1: 91,043,635 (GRCm39)	T680I	probably benign	Het
Lypd10	T	A	7: 24,411,954 (GRCm39)	W45R	probably damaging	Het
Map3k19	T	A	1: 127,758,010 (GRCm39)	D186V	possibly damaging	Het
Mrgprx2	T	C	7: 48,132,374 (GRCm39)	Y148C	probably damaging	Het
Muc4	G	A	16: 32,569,473 (GRCm39)	A178T	probably benign	Het
Mylip	A	C	13: 45,543,479 (GRCm39)	E16A	probably benign	Het
Nek9	A	G	12: 85,352,379 (GRCm39)	F828S	probably damaging	Het
Obscn	A	G	11: 58,928,631 (GRCm39)	F6012L	probably damaging	Het
Or14a257	A	G	7: 86,138,139 (GRCm39)	S207P	possibly damaging	Het
Or2o1	A	C	11: 49,051,438 (GRCm39)	D199A	probably damaging	Het
Or5p54	A	G	7: 107,554,580 (GRCm39)	Y244C	possibly damaging	Het
Pcid2	T	A	8: 13,129,936 (GRCm39)	K273N	possibly damaging	Het
Plekhm3	C	T	1: 64,960,991 (GRCm39)	D422N	probably damaging	Het
Prr12	T	C	7: 44,692,909 (GRCm39)	H1541R	probably damaging	Het
Psg26	A	C	7: 18,209,028 (GRCm39)	V460G	probably damaging	Het
Rbmxl1	G	A	8: 79,232,459 (GRCm39)	R295*	probably null	Het
Sbf1	A	T	15: 89,187,481 (GRCm39)	V690E	probably damaging	Het
Serpinb2	T	A	1: 107,449,910 (GRCm39)	S108T	probably benign	Het
Sin3b	T	C	8: 73,476,692 (GRCm39)	Y709H	probably damaging	Het
Slc17a5	A	G	9: 78,481,989 (GRCm39)	W160R	probably damaging	Het
Spef2	T	A	15: 9,704,466 (GRCm39)	D449V	probably damaging	Het
Tas2r108	C	A	6: 40,470,720 (GRCm39)	N65K	possibly damaging	Het
Tex15	T	A	8: 34,063,575 (GRCm39)	F1002I	possibly damaging	Het
Trpm5	G	A	7: 142,629,338 (GRCm39)	S942L	probably benign	Het
Tspan5	T	C	3: 138,596,517 (GRCm39)	S52P	probably damaging	Het
Uqcrfs1	T	C	13: 30,725,181 (GRCm39)	T120A	probably benign	Het
Usp6nl	T	C	2: 6,428,246 (GRCm39)	F193L	probably damaging	Het
Vmn2r26	T	A	6: 124,030,833 (GRCm39)	C523S	probably damaging	Het
Wfdc2	C	T	2: 164,405,979 (GRCm39)	P92S	probably benign	Het
Zbtb18	A	T	1: 177,275,549 (GRCm39)	H303L	probably benign	Het
Zfp174	A	T	16: 3,672,153 (GRCm39)	H234L	probably benign	Het
Zmynd12	T	C	4: 119,299,117 (GRCm39)		probably null	Het

Other mutations in Ldb1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
R1585:Ldb1	UTSW	19	46,022,903 (GRCm39)	missense	probably damaging	0.99
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

Posted On

2013-12-09