Mutagenetix > Incidental Mutation

Incidental Mutation 'R7132:Ldb3'

552768

Institutional Source

Beutler Lab

Gene Symbol

Ldb3

Ensembl Gene

ENSMUSG00000021798

Gene Name

LIM domain binding 3

Synonyms

ZASP, cypher

MMRRC Submission

045217-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7132 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

34248560-34310639 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 34298992 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 211 (Y211H)

Ref Sequence

ENSEMBL: ENSMUSP00000022327 (fasta)

Gene Model

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

AlphaFold

Q9JKS4

PDB Structure

Solution structure of PDZ domain of mouse Cypher protein [SOLUTION NMR]

Predicted Effect

probably benign
Transcript: ENSMUST00000022327
AA Change: Y211H

PolyPhen 2 Score 0.246 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000022327
Gene: ENSMUSG00000021798
AA Change: Y211H

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

probably benign
Transcript: ENSMUST00000022328
AA Change: Y211H

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000022328
Gene: ENSMUSG00000021798
AA Change: Y211H

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

probably benign
Transcript: ENSMUST00000022330
AA Change: Y211H

PolyPhen 2 Score 0.381 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000022330
Gene: ENSMUSG00000021798
AA Change: Y211H

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 benign
Transcript: ENSMUST00000064098

SMART Domains

Protein: ENSMUSP00000066784
Gene: ENSMUSG00000021798

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

SMART Domains

Protein: ENSMUSP00000087494
Gene: ENSMUSG00000021798

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

probably benign
Transcript: ENSMUST00000227819

Predicted Effect

probably benign
Transcript: ENSMUST00000228044

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ank3	C	T	10: 69,825,744 (GRCm39)	A1471V		Het
Ankrd12	C	A	17: 66,290,242 (GRCm39)	M1730I	probably benign	Het
Ap2a2	T	C	7: 141,199,478 (GRCm39)	Y462H	probably benign	Het
Ap5b1	T	A	19: 5,619,412 (GRCm39)	Y277*	probably null	Het
App	T	C	16: 84,853,370 (GRCm39)	D236G	unknown	Het
Arid2	A	T	15: 96,247,894 (GRCm39)	K102I	possibly damaging	Het
Asl	A	G	5: 130,043,543 (GRCm39)	V211A	possibly damaging	Het
Card6	TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG	TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG	15: 5,128,173 (GRCm39)		probably benign	Het
Cbx2	A	G	11: 118,913,947 (GRCm39)	S5G	probably benign	Het
Ccdc183	A	G	2: 25,506,542 (GRCm39)		probably null	Het
Cd72	T	C	4: 43,452,444 (GRCm39)	Q183R	possibly damaging	Het
Cdh26	T	A	2: 178,128,555 (GRCm39)	D702E	possibly damaging	Het
Cfap61	A	T	2: 145,951,870 (GRCm39)	N784I	probably damaging	Het
Cgrrf1	G	A	14: 47,091,321 (GRCm39)	V282M	probably damaging	Het
Cmtm1	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	8: 105,036,102 (GRCm39)		probably benign	Het
Cobll1	T	G	2: 64,964,112 (GRCm39)	K170Q	probably damaging	Het
Copg2	A	T	6: 30,792,931 (GRCm39)	V468D	probably benign	Het
Cracr2b	C	T	7: 141,043,651 (GRCm39)	A84V	probably benign	Het
Cyp2f2	A	T	7: 26,831,993 (GRCm39)	D416V	probably benign	Het
Dcaf10	T	C	4: 45,342,391 (GRCm39)	F75S	probably benign	Het
Eml3	G	T	19: 8,918,392 (GRCm39)	A829S	probably benign	Het
Entpd3	A	G	9: 120,390,086 (GRCm39)	T402A	probably benign	Het
Fer1l4	A	T	2: 155,887,546 (GRCm39)	V550E	probably damaging	Het
Fgb	G	A	3: 82,954,053 (GRCm39)	R62*	probably null	Het
Fubp1	T	A	3: 151,937,661 (GRCm39)		probably null	Het
Gdf3	A	C	6: 122,583,283 (GRCm39)	D361E	probably damaging	Het
Gm6685	A	T	11: 28,289,330 (GRCm39)	I162N	probably damaging	Het
Hmx2	A	G	7: 131,157,645 (GRCm39)	Y253C	probably damaging	Het
Ints2	G	T	11: 86,108,580 (GRCm39)	N922K	probably benign	Het
Ipo7	C	T	7: 109,653,254 (GRCm39)	L984F	probably benign	Het
Itgae	A	T	11: 73,002,184 (GRCm39)	Y96F	possibly damaging	Het
Kalrn	A	G	16: 34,076,597 (GRCm39)	V697A	unknown	Het
Kctd18	G	A	1: 58,006,737 (GRCm39)	R38*	probably null	Het
Kdm5b	A	G	1: 134,526,844 (GRCm39)	D322G	probably damaging	Het
Limch1	T	C	5: 67,111,028 (GRCm39)	F85S	probably damaging	Het
Lrrn4	A	T	2: 132,721,613 (GRCm39)	L68*	probably null	Het
Lrwd1	A	G	5: 136,152,129 (GRCm39)	V616A	possibly damaging	Het
Nars1	A	G	18: 64,640,841 (GRCm39)		probably null	Het
Nradd	T	C	9: 110,451,329 (GRCm39)	D13G	probably benign	Het
Oacyl	A	T	18: 65,831,480 (GRCm39)	N39I	probably damaging	Het
Onecut2	A	T	18: 64,473,983 (GRCm39)	H178L	possibly damaging	Het
Or9i14	T	A	19: 13,792,786 (GRCm39)	Q56L	probably benign	Het
Pcdhga4	A	C	18: 37,820,430 (GRCm39)	T660P	probably damaging	Het
Peg10	CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG	CCACATCAGGATCCACATCAGGATGCACATCAG	6: 4,756,398 (GRCm39)		probably benign	Het
Pitpnm3	T	A	11: 71,942,102 (GRCm39)	I902F	possibly damaging	Het
Plod3	T	C	5: 137,023,971 (GRCm39)	L180S		Het
Prrc2c	A	T	1: 162,508,850 (GRCm39)	H2354Q	possibly damaging	Het
Pth2r	A	G	1: 65,361,225 (GRCm39)	E58G	probably benign	Het
Rev1	G	T	1: 38,110,530 (GRCm39)	D573E	possibly damaging	Het
Sec24a	A	T	11: 51,605,963 (GRCm39)	L696*	probably null	Het
Serpinb3c	A	G	1: 107,204,681 (GRCm39)	S22P	probably damaging	Het
St18	A	T	1: 6,929,351 (GRCm39)	H81L		Het
Stard9	A	T	2: 120,509,859 (GRCm39)	K266*	probably null	Het
Stip1	C	T	19: 6,999,178 (GRCm39)	G467S	possibly damaging	Het
Syne1	G	A	10: 5,193,180 (GRCm39)	A3956V	probably damaging	Het
Tcp10a	C	T	17: 7,612,351 (GRCm39)	T381I	probably benign	Het
Tecpr2	T	A	12: 110,881,806 (GRCm39)	V125D	probably damaging	Het
Tmc2	T	C	2: 130,074,329 (GRCm39)	S341P	possibly damaging	Het
Tmem190	G	A	7: 4,787,224 (GRCm39)	V143I	probably benign	Het
Trap1	A	G	16: 3,873,693 (GRCm39)	Y288H	probably benign	Het
Trim39	T	C	17: 36,571,547 (GRCm39)	T404A	probably benign	Het
Ttn	T	A	2: 76,576,043 (GRCm39)	K24950I	probably damaging	Het
Ttn	G	T	2: 76,774,696 (GRCm39)	N2161K	unknown	Het
Unc13b	T	C	4: 43,215,757 (GRCm39)	S19P	probably benign	Het
Uqcrc1	T	A	9: 108,778,536 (GRCm39)	I471N	probably damaging	Het
Wbp11	T	C	6: 136,798,540 (GRCm39)	T170A	probably benign	Het
Wnk4	A	G	11: 101,152,026 (GRCm39)	I177V	probably benign	Het
Zfp455	C	A	13: 67,347,230 (GRCm39)	P51T	probably damaging	Het
Zfp946	T	C	17: 22,673,644 (GRCm39)	Y133H	probably benign	Het
Zfp955a	A	T	17: 33,460,589 (GRCm39)	Y514*	probably null	Het
Zzef1	T	C	11: 72,808,697 (GRCm39)		probably null	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
R4963:Ldb3	UTSW	14	34,288,815 (GRCm39)	missense	probably damaging	0.98
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
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'- ACAGCGGACTCAATGGGATC -3'
(R):5'- AGTTCGGGGACACCTTTAGC -3'

Sequencing Primer
(F):5'- ACTCAATGGGATCCCTGCTG -3'
(R):5'- GGGGACACCTTTAGCTCCTC -3'

Posted On

2019-05-15