Mutagenetix > Incidental Mutation

Incidental Mutation 'R1524:Ldb3'

167740

Institutional Source

Beutler Lab

Gene Symbol

Ldb3

Ensembl Gene

ENSMUSG00000021798

Gene Name

LIM domain binding 3

Synonyms

ZASP, cypher

MMRRC Submission

039565-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1524 (G1)

Quality Score

208

Status

Validated

Chromosome

Chromosomal Location

34248560-34310639 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 34277313 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Leucine at position 354 (V354L)

Ref Sequence

ENSEMBL: ENSMUSP00000022327 (fasta)

Gene Model

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

AlphaFold

Q9JKS4

PDB Structure

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

Predicted Effect

probably benign
Transcript: ENSMUST00000022327
AA Change: V354L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000022327
Gene: ENSMUSG00000021798
AA Change: V354L

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

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

probably benign
Transcript: ENSMUST00000064098
AA Change: V310L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000066784
Gene: ENSMUSG00000021798
AA Change: V310L

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: V315L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000087494
Gene: ENSMUSG00000021798
AA Change: V315L

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: ENSMUST00000228044

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.5%

Validation Efficiency

97% (68/70)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310003L06Rik	G	T	5: 88,119,548 (GRCm39)	V102L	probably benign	Het
Adck1	T	C	12: 88,368,854 (GRCm39)	Y111H	probably damaging	Het
Adcy10	G	T	1: 165,345,972 (GRCm39)	K340N	probably damaging	Het
Aebp1	T	C	11: 5,820,089 (GRCm39)	V355A	probably damaging	Het
Atp2b2	T	C	6: 113,751,162 (GRCm39)		probably benign	Het
Atrn	T	C	2: 130,799,000 (GRCm39)	V390A	probably benign	Het
Bpifc	T	A	10: 85,813,599 (GRCm39)	Q315L	probably benign	Het
C1qtnf6	T	G	15: 78,409,092 (GRCm39)		probably null	Het
Cab39l	A	G	14: 59,757,186 (GRCm39)		probably benign	Het
Capn12	T	A	7: 28,582,189 (GRCm39)		probably benign	Het
Ceacam18	A	C	7: 43,288,779 (GRCm39)	T177P	possibly damaging	Het
Ces5a	A	T	8: 94,252,293 (GRCm39)	F200I	probably damaging	Het
Cldn19	G	T	4: 119,114,248 (GRCm39)		probably null	Het
Cntnap2	A	G	6: 46,507,613 (GRCm39)	S46P	probably damaging	Het
Dchs1	A	G	7: 105,413,732 (GRCm39)	Y1028H	probably damaging	Het
Exd1	A	T	2: 119,355,155 (GRCm39)	F253L	probably damaging	Het
Fam161a	A	G	11: 22,965,826 (GRCm39)	N40D	possibly damaging	Het
Fam81a	A	T	9: 70,032,390 (GRCm39)	I34N	probably damaging	Het
Fchsd1	A	C	18: 38,098,950 (GRCm39)		probably null	Het
Fut11	T	A	14: 20,746,234 (GRCm39)	F359I	possibly damaging	Het
Fut7	T	C	2: 25,315,159 (GRCm39)	V92A	probably damaging	Het
Grid2	C	G	6: 64,406,738 (GRCm39)	F699L	possibly damaging	Het
Grin2a	A	G	16: 9,481,467 (GRCm39)	S445P	possibly damaging	Het
H2al2b	A	C	Y: 2,720,391 (GRCm39)	F95C	probably damaging	Het
Hecw2	T	C	1: 53,890,777 (GRCm39)	D1246G	probably damaging	Het
Ifit1	A	G	19: 34,625,032 (GRCm39)	N56S	probably damaging	Het
Lrig2	T	C	3: 104,371,192 (GRCm39)	Y479C	probably benign	Het
Ltn1	A	G	16: 87,178,444 (GRCm39)	V1595A	probably damaging	Het
Macf1	A	G	4: 123,326,323 (GRCm39)	V2939A	possibly damaging	Het
Mapre3	T	G	5: 31,019,261 (GRCm39)	I35S	probably damaging	Het
Med16	A	T	10: 79,734,150 (GRCm39)	L588Q	probably damaging	Het
Ncapg2	T	C	12: 116,398,198 (GRCm39)		probably benign	Het
Ncstn	C	A	1: 171,899,716 (GRCm39)	R322L	possibly damaging	Het
Ndst1	A	T	18: 60,831,576 (GRCm39)	I594N	probably damaging	Het
Ndst3	A	G	3: 123,342,555 (GRCm39)	I752T	possibly damaging	Het
Obscn	G	T	11: 59,006,681 (GRCm39)	S1185R	probably damaging	Het
Or5b112	T	A	19: 13,319,486 (GRCm39)	C121*	probably null	Het
Or6aa1	A	G	7: 86,044,020 (GRCm39)	S229P	probably benign	Het
Or9q1	A	T	19: 13,805,679 (GRCm39)	L27H	probably damaging	Het
Otof	T	A	5: 30,536,900 (GRCm39)	D1285V	probably benign	Het
Pcnx2	A	G	8: 126,617,880 (GRCm39)	I125T	probably benign	Het
Pde4a	T	C	9: 21,112,543 (GRCm39)	S240P	probably damaging	Het
Pi15	T	C	1: 17,690,076 (GRCm39)	S126P	probably benign	Het
Pkhd1	T	C	1: 20,188,004 (GRCm39)	S3435G	probably damaging	Het
Plin1	C	A	7: 79,376,338 (GRCm39)	V133L	probably benign	Het
Pnpt1	T	A	11: 29,080,776 (GRCm39)	C7S	unknown	Het
Ppp3ca	A	T	3: 136,503,579 (GRCm39)	M51L	probably benign	Het
Primpol	G	T	8: 47,039,502 (GRCm39)		probably benign	Het
Prlr	T	C	15: 10,319,419 (GRCm39)	V116A	probably damaging	Het
Ptgr3	A	G	18: 84,112,831 (GRCm39)	E169G	probably benign	Het
Rnf139	A	G	15: 58,761,266 (GRCm39)	D35G	probably damaging	Het
Rsbn1l	T	A	5: 21,156,671 (GRCm39)	K38M	probably damaging	Het
Ryr3	T	A	2: 112,699,427 (GRCm39)	I888F	probably damaging	Het
Sec16a	C	A	2: 26,318,394 (GRCm39)	V1566F	probably damaging	Het
Sin3b	A	G	8: 73,479,915 (GRCm39)	T874A	probably benign	Het
Skic3	T	A	13: 76,286,491 (GRCm39)	D891E	probably benign	Het
Slc5a5	A	C	8: 71,344,978 (GRCm39)	Y110D	probably damaging	Het
Smarcd2	C	T	11: 106,157,978 (GRCm39)	V97I	probably benign	Het
St6galnac2	G	A	11: 116,575,313 (GRCm39)		probably benign	Het
Tbc1d22b	T	C	17: 29,789,585 (GRCm39)	L149P	probably damaging	Het
Tekt2	T	C	4: 126,217,442 (GRCm39)	I208V	probably benign	Het
Tenm3	A	G	8: 48,682,016 (GRCm39)	I2522T	possibly damaging	Het
Ttll5	T	A	12: 85,911,342 (GRCm39)	Y233*	probably null	Het
Vcpip1	C	T	1: 9,794,727 (GRCm39)	E1215K	probably damaging	Het
Wdr4	T	C	17: 31,728,737 (GRCm39)		probably benign	Het
Zfp703	G	A	8: 27,469,401 (GRCm39)	G355D	probably damaging	Het
Zfp830	T	A	11: 82,655,794 (GRCm39)	D199E	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
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
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'- CACTAATCATGGCTCGTGCATCCC -3'
(R):5'- ACTGCCCTGTAGTTTGCTGAGAAAG -3'

Sequencing Primer
(F):5'- GCTCGTGCATCCCATACAATAG -3'
(R):5'- AGATTAAGTTGTCAGACCCCTC -3'

Posted On

2014-04-13