Mutagenetix > Incidental Mutation

Incidental Mutation 'R4963:Ldb3'

444545

Institutional Source

Beutler Lab

Gene Symbol

Ldb3

Ensembl Gene

ENSMUSG00000021798

Gene Name

LIM domain binding 3

Synonyms

ZASP, cypher

MMRRC Submission

042560-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4963 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34248560-34310639 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 34288815 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 252 (S252R)

Ref Sequence

ENSEMBL: ENSMUSP00000066784 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000022327] [ENSMUST00000022328] [ENSMUST00000022330] [ENSMUST00000064098] [ENSMUST00000090040] [ENSMUST00000227819] [ENSMUST00000228044]

AlphaFold

Q9JKS4

Predicted Effect

probably benign
Transcript: ENSMUST00000022327
AA Change: S296R

PolyPhen 2 Score 0.323 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000022327
Gene: ENSMUSG00000021798
AA Change: S296R

Domain	Start	End	E-Value	Type
PDZ	11	84	1.68e-16	SMART
low complexity region	138	147	N/A	INTRINSIC
ZM	186	211	1.33e-8	SMART
low complexity region	214	229	N/A	INTRINSIC
low complexity region	309	353	N/A	INTRINSIC
low complexity region	359	376	N/A	INTRINSIC
low complexity region	418	473	N/A	INTRINSIC
LIM	546	597	2.72e-16	SMART
LIM	605	656	2.65e-19	SMART
LIM	664	717	1.04e-17	SMART

Predicted Effect

silent
Transcript: ENSMUST00000022328

SMART Domains

Protein: ENSMUSP00000022328
Gene: ENSMUSG00000021798

Domain	Start	End	E-Value	Type
PDZ	11	84	1.68e-16	SMART
low complexity region	138	147	N/A	INTRINSIC
ZM	186	211	1.33e-8	SMART
low complexity region	214	229	N/A	INTRINSIC
low complexity region	297	314	N/A	INTRINSIC
low complexity region	356	411	N/A	INTRINSIC
LIM	484	535	2.72e-16	SMART
LIM	543	594	2.65e-19	SMART
LIM	602	655	1.04e-17	SMART

Predicted Effect

silent
Transcript: ENSMUST00000022330

SMART Domains

Protein: ENSMUSP00000022330
Gene: ENSMUSG00000021798

Domain	Start	End	E-Value	Type
PDZ	11	84	1.68e-16	SMART
low complexity region	138	147	N/A	INTRINSIC
ZM	186	211	1.33e-8	SMART
low complexity region	214	229	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000064098
AA Change: S252R

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000066784
Gene: ENSMUSG00000021798
AA Change: S252R

Domain	Start	End	E-Value	Type
PDZ	11	84	1.68e-16	SMART
ZM	148	173	5.18e-11	SMART
low complexity region	265	309	N/A	INTRINSIC
low complexity region	315	332	N/A	INTRINSIC
low complexity region	374	429	N/A	INTRINSIC
LIM	502	553	2.72e-16	SMART
LIM	561	612	2.65e-19	SMART
LIM	620	673	1.04e-17	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000090040
AA Change: S257R

PolyPhen 2 Score 0.118 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000087494
Gene: ENSMUSG00000021798
AA Change: S257R

Domain	Start	End	E-Value	Type
PDZ	11	84	1.68e-16	SMART
ZM	148	173	5.18e-11	SMART
low complexity region	270	314	N/A	INTRINSIC
low complexity region	320	337	N/A	INTRINSIC
low complexity region	379	434	N/A	INTRINSIC
LIM	507	558	2.72e-16	SMART
LIM	566	617	2.65e-19	SMART
LIM	625	678	1.04e-17	SMART

Predicted Effect

silent
Transcript: ENSMUST00000227819

Predicted Effect

silent
Transcript: ENSMUST00000228044

Meta Mutation Damage Score

0.0920

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.3%

Validation Efficiency

97% (74/76)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]
PHENOTYPE: Homozygous mutation of this gene results in lethality within a few days after birth from muscle abnormalities. Mutant mice exhibit myopathy, dysphagia, heart vascular congestion, dilated heart ventricles, cyanosis, and respiratory distress. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A530064D06Rik	A	T	17: 48,470,582 (GRCm39)	I133N	probably benign	Het
Abca15	T	C	7: 119,960,142 (GRCm39)	S642P	probably damaging	Het
Abcg5	G	T	17: 84,967,569 (GRCm39)	Y410*	probably null	Het
Anapc7	T	A	5: 122,560,669 (GRCm39)	M10K	probably damaging	Het
Ank2	G	A	3: 126,825,745 (GRCm39)	T418M	probably benign	Het
Arhgap17	T	C	7: 122,907,583 (GRCm39)	R260G	possibly damaging	Het
Atp1a3	T	C	7: 24,694,051 (GRCm39)	T381A	probably damaging	Het
Cep89	T	G	7: 35,102,577 (GRCm39)	S97A	probably benign	Het
Cyp2j11	T	C	4: 96,204,619 (GRCm39)	D309G	probably damaging	Het
Dcbld2	T	C	16: 58,286,145 (GRCm39)	I768T	probably benign	Het
Defa41	C	T	8: 21,691,774 (GRCm39)	S52F	probably damaging	Het
Dgke	A	G	11: 88,941,628 (GRCm39)	V249A	possibly damaging	Het
Dnah9	T	C	11: 65,975,437 (GRCm39)		probably null	Het
Dnajc3	C	A	14: 119,215,585 (GRCm39)	H502N	probably benign	Het
Dsp	A	G	13: 38,381,846 (GRCm39)	T2265A	probably damaging	Het
Enpp6	A	G	8: 47,518,496 (GRCm39)	D208G	probably benign	Het
Evc	C	T	5: 37,479,393 (GRCm39)		probably null	Het
Fam98a	A	G	17: 75,845,977 (GRCm39)	S285P	probably damaging	Het
Glp2r	G	T	11: 67,648,419 (GRCm39)	Y94*	probably null	Het
Gsdmc	A	G	15: 63,676,229 (GRCm39)		probably null	Het
Gtpbp4	C	A	13: 9,035,253 (GRCm39)	D369Y	probably damaging	Het
H2-M1	A	G	17: 36,982,630 (GRCm39)	Y77H	probably benign	Het
Irx2	T	C	13: 72,780,729 (GRCm39)	V466A	possibly damaging	Het
Kcnh4	C	A	11: 100,643,079 (GRCm39)	W396L	probably damaging	Het
Kif27	T	C	13: 58,476,808 (GRCm39)	D614G	possibly damaging	Het
Kirrel2	C	A	7: 30,150,226 (GRCm39)		probably null	Het
Lcn5	A	G	2: 25,551,426 (GRCm39)	I182V	probably benign	Het
Marchf8	G	A	6: 116,363,232 (GRCm39)		probably benign	Het
Mdn1	C	A	4: 32,756,512 (GRCm39)	Q4735K	probably benign	Het
Mfrp	A	T	9: 44,014,561 (GRCm39)	H236L	probably benign	Het
Mlph	A	G	1: 90,867,112 (GRCm39)	D378G	probably damaging	Het
Msi1	T	A	5: 115,588,944 (GRCm39)	Y320N	probably damaging	Het
Mtmr11	T	C	3: 96,070,567 (GRCm39)		probably benign	Het
Mtpap	T	C	18: 4,375,638 (GRCm39)	V6A	probably benign	Het
Nedd1	C	A	10: 92,530,893 (GRCm39)	D399Y	probably damaging	Het
Ninl	A	G	2: 150,781,829 (GRCm39)	Y234H	probably benign	Het
Nkx3-1	G	A	14: 69,428,367 (GRCm39)	G72S	probably benign	Het
Nle1	A	G	11: 82,795,763 (GRCm39)	V228A	probably benign	Het
Npy4r	T	A	14: 33,868,973 (GRCm39)	D105V	probably damaging	Het
Or1f12	A	G	13: 21,722,152 (GRCm39)	Y8H	probably damaging	Het
Palld	C	T	8: 62,156,244 (GRCm39)	V464M	probably damaging	Het
Pclo	T	C	5: 14,719,235 (GRCm39)	V1124A	unknown	Het
Pex1	T	A	5: 3,659,924 (GRCm39)	M476K	probably benign	Het
Pkhd1l1	G	A	15: 44,367,421 (GRCm39)	S773N	probably benign	Het
Polrmt	A	G	10: 79,582,385 (GRCm39)	M1T	probably null	Het
Prmt9	A	G	8: 78,282,358 (GRCm39)	D85G	probably damaging	Het
Ptpn12	T	A	5: 21,220,706 (GRCm39)		probably null	Het
Rbm19	T	A	5: 120,279,631 (GRCm39)	M766K	probably damaging	Het
Rdh11	A	G	12: 79,235,380 (GRCm39)	V72A	probably benign	Het
Rxfp3	A	G	15: 11,036,367 (GRCm39)	V335A	probably damaging	Het
Sema6a	T	C	18: 47,431,318 (GRCm39)	K127E	possibly damaging	Het
Slc5a1	C	T	5: 33,318,126 (GRCm39)	T593I	probably benign	Het
Slco1a1	A	G	6: 141,868,825 (GRCm39)	F380L	probably benign	Het
Smc2	T	C	4: 52,450,826 (GRCm39)	S215P	probably damaging	Het
Smyd2	A	T	1: 189,614,385 (GRCm39)	V381E	probably damaging	Het
Smyd4	C	T	11: 75,273,120 (GRCm39)	S60L	probably benign	Het
Spata18	T	A	5: 73,836,336 (GRCm39)	V419E	probably damaging	Het
Terb1	A	G	8: 105,208,950 (GRCm39)	L376S	probably damaging	Het
Timd2	T	C	11: 46,573,617 (GRCm39)	E129G	possibly damaging	Het
Topbp1	C	A	9: 103,197,804 (GRCm39)	T461K	probably benign	Het
Tpp2	G	A	1: 44,031,428 (GRCm39)	R1069Q	probably damaging	Het
Ttn	A	G	2: 76,584,289 (GRCm39)	V22273A	probably damaging	Het
Tulp4	G	A	17: 6,249,088 (GRCm39)	E36K	probably damaging	Het
Uqcrfs1	A	T	13: 30,724,746 (GRCm39)	F265I	probably damaging	Het
Vmn2r107	A	T	17: 20,595,403 (GRCm39)	Q652L	probably damaging	Het
Vwf	C	T	6: 125,644,446 (GRCm39)	R2434*	probably null	Het
Wdhd1	A	G	14: 47,506,146 (GRCm39)	V256A	possibly damaging	Het
Zfp442	A	T	2: 150,250,415 (GRCm39)	C439S	probably damaging	Het
Zfp709	A	G	8: 72,643,632 (GRCm39)	T354A	probably benign	Het
Zswim2	A	T	2: 83,755,454 (GRCm39)	I149N	probably damaging	Het

Other mutations in Ldb3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01124:Ldb3	APN	14	34,266,157 (GRCm39)	missense	probably damaging	0.99
IGL01485:Ldb3	APN	14	34,264,519 (GRCm39)	missense	probably damaging	1.00
IGL01983:Ldb3	APN	14	34,299,156 (GRCm39)	missense	probably benign	0.00
R0323:Ldb3	UTSW	14	34,266,002 (GRCm39)	missense	probably damaging	1.00
R0335:Ldb3	UTSW	14	34,300,608 (GRCm39)	missense	possibly damaging	0.77
R0483:Ldb3	UTSW	14	34,258,541 (GRCm39)	missense	probably damaging	1.00
R0920:Ldb3	UTSW	14	34,289,460 (GRCm39)	missense	probably benign	0.05
R1524:Ldb3	UTSW	14	34,277,313 (GRCm39)	missense	probably benign	0.01
R2161:Ldb3	UTSW	14	34,289,353 (GRCm39)	critical splice donor site	probably null
R2246:Ldb3	UTSW	14	34,251,432 (GRCm39)	missense	probably damaging	0.99
R2865:Ldb3	UTSW	14	34,251,460 (GRCm39)	missense	probably damaging	1.00
R3113:Ldb3	UTSW	14	34,251,418 (GRCm39)	makesense	probably null
R3765:Ldb3	UTSW	14	34,300,639 (GRCm39)	splice site	probably null
R3870:Ldb3	UTSW	14	34,289,440 (GRCm39)	missense	probably damaging	1.00
R4018:Ldb3	UTSW	14	34,274,128 (GRCm39)	splice site	probably benign
R4797:Ldb3	UTSW	14	34,277,470 (GRCm39)	missense	possibly damaging	0.95
R5705:Ldb3	UTSW	14	34,298,986 (GRCm39)	missense	probably null	0.01
R6401:Ldb3	UTSW	14	34,299,291 (GRCm39)	missense	probably benign	0.33
R6549:Ldb3	UTSW	14	34,263,854 (GRCm39)	missense	probably damaging	0.99
R6682:Ldb3	UTSW	14	34,274,221 (GRCm39)	missense	possibly damaging	0.77
R6917:Ldb3	UTSW	14	34,277,321 (GRCm39)	missense	probably null	0.03
R7132:Ldb3	UTSW	14	34,298,992 (GRCm39)	missense	probably benign	0.25
R7327:Ldb3	UTSW	14	34,293,759 (GRCm39)	missense	probably damaging	1.00
R7488:Ldb3	UTSW	14	34,289,402 (GRCm39)	missense	probably damaging	1.00
R7760:Ldb3	UTSW	14	34,264,460 (GRCm39)	missense	probably damaging	1.00
R8755:Ldb3	UTSW	14	34,299,256 (GRCm39)	missense	probably damaging	1.00
R8845:Ldb3	UTSW	14	34,258,634 (GRCm39)	missense	probably damaging	1.00
R8954:Ldb3	UTSW	14	34,277,301 (GRCm39)	missense	probably null	0.17
R9179:Ldb3	UTSW	14	34,277,312 (GRCm39)	missense	probably benign
R9321:Ldb3	UTSW	14	34,266,099 (GRCm39)	nonsense	probably null
R9702:Ldb3	UTSW	14	34,299,090 (GRCm39)	missense	probably benign	0.03
Z1176:Ldb3	UTSW	14	34,277,322 (GRCm39)	missense	probably benign	0.21
Z1177:Ldb3	UTSW	14	34,266,060 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TATTCTCCAAAGCCCAGTGAAGG -3'
(R):5'- CACAGGAAGTGTTTAGGGCC -3'

Sequencing Primer
(F):5'- CTCTACCTTGGTGACCTGGGAAAG -3'
(R):5'- TATGTTCGCTGTGAGTCC -3'

Posted On

2016-11-14