Mutagenetix > Incidental Mutation

Incidental Mutation 'R4797:Ldb3'

369162

Institutional Source

Beutler Lab

Gene Symbol

Ldb3

Ensembl Gene

ENSMUSG00000021798

Gene Name

LIM domain binding 3

Synonyms

ZASP, cypher

MMRRC Submission

042421-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4797 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34248560-34310639 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 34277470 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 262 (H262Q)

Ref Sequence

ENSEMBL: ENSMUSP00000087494 (fasta)

Gene Model

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

AlphaFold

Q9JKS4

Predicted Effect

probably benign
Transcript: ENSMUST00000022327
AA Change: H301Q

PolyPhen 2 Score 0.250 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000022327
Gene: ENSMUSG00000021798
AA Change: H301Q

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

possibly damaging
Transcript: ENSMUST00000064098
AA Change: H257Q

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000066784
Gene: ENSMUSG00000021798
AA Change: H257Q

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

possibly damaging
Transcript: ENSMUST00000090040
AA Change: H262Q

PolyPhen 2 Score 0.953 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000087494
Gene: ENSMUSG00000021798
AA Change: H262Q

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

0.0673

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.8%

Validation Efficiency

96% (69/72)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	T	C	11: 110,008,945 (GRCm39)	T1195A	probably benign	Het
Apobr	G	A	7: 126,186,756 (GRCm39)	E756K	probably benign	Het
Arpc3	A	G	5: 122,542,215 (GRCm39)	E77G	possibly damaging	Het
Atp2b2	A	T	6: 113,766,847 (GRCm39)	M464K	possibly damaging	Het
Atxn7l2	A	G	3: 108,111,866 (GRCm39)	S379P	probably damaging	Het
Ccdc91	A	T	6: 147,493,641 (GRCm39)	E344D	unknown	Het
Cdc42bpg	G	A	19: 6,370,477 (GRCm39)	R1190Q	probably damaging	Het
Cdh17	C	A	4: 11,810,390 (GRCm39)	Q694K	probably benign	Het
Chordc1	G	T	9: 18,203,672 (GRCm39)		probably benign	Het
Copg1	A	G	6: 87,880,450 (GRCm39)		probably benign	Het
Dcbld1	T	C	10: 52,160,223 (GRCm39)	V37A	probably damaging	Het
Ddb2	A	G	2: 91,067,163 (GRCm39)		probably benign	Het
Dok5	A	T	2: 170,672,042 (GRCm39)	R115*	probably null	Het
Drc7	T	C	8: 95,800,925 (GRCm39)	I649T	probably damaging	Het
Efr3a	A	G	15: 65,729,437 (GRCm39)	T713A	probably damaging	Het
Epg5	G	A	18: 78,073,614 (GRCm39)	D2494N	probably benign	Het
Eps15	G	A	4: 109,223,727 (GRCm39)		probably benign	Het
Glb1l3	T	C	9: 26,739,742 (GRCm39)	D356G	probably damaging	Het
Gm1818	A	T	12: 48,602,393 (GRCm39)		noncoding transcript	Het
Gsta5	A	T	9: 78,211,679 (GRCm39)	Y147F	probably benign	Het
Hcrtr2	C	A	9: 76,161,816 (GRCm39)	M191I	probably damaging	Het
Heatr1	G	A	13: 12,426,929 (GRCm39)	E685K	probably benign	Het
Hsd3b2	A	T	3: 98,618,979 (GRCm39)	L322Q	probably damaging	Het
Hsd3b9	T	A	3: 98,363,747 (GRCm39)	R62*	probably null	Het
Htra4	T	C	8: 25,523,675 (GRCm39)	T297A	probably damaging	Het
Il22	C	A	10: 118,041,058 (GRCm39)	R55S	probably damaging	Het
Ints1	G	A	5: 139,757,631 (GRCm39)	T324M	possibly damaging	Het
Ints15	A	G	5: 143,297,504 (GRCm39)	F181S	probably benign	Het
Ints7	T	C	1: 191,329,045 (GRCm39)	V268A	probably damaging	Het
Kctd20	G	A	17: 29,185,766 (GRCm39)	V370I	probably damaging	Het
Lama1	T	A	17: 68,023,770 (GRCm39)	M55K	probably benign	Het
Larp1	C	A	11: 57,938,806 (GRCm39)	S494*	probably null	Het
Lepr	C	A	4: 101,637,244 (GRCm39)	T711K	possibly damaging	Het
Mon2	T	C	10: 122,852,422 (GRCm39)	I984V	probably benign	Het
Naip2	T	A	13: 100,298,243 (GRCm39)	S598C	probably damaging	Het
Oasl1	A	G	5: 115,066,217 (GRCm39)	M112V	probably benign	Het
Or2d2b	A	T	7: 106,705,234 (GRCm39)	M278K	probably benign	Het
Or6c214	A	T	10: 129,590,390 (GRCm39)	S310T	probably benign	Het
Or7c19	G	T	8: 85,957,567 (GRCm39)	A148S	probably benign	Het
P2ry1	T	A	3: 60,910,881 (GRCm39)	S7T	probably benign	Het
Pidd1	G	T	7: 141,022,899 (GRCm39)	R98S	possibly damaging	Het
Pkd1l1	A	C	11: 8,911,340 (GRCm39)	F312L	unknown	Het
Pla2r1	A	T	2: 60,334,524 (GRCm39)	M416K	possibly damaging	Het
Pold1	T	C	7: 44,191,325 (GRCm39)	E194G	possibly damaging	Het
Poldip2	T	A	11: 78,404,813 (GRCm39)	Y77N	probably damaging	Het
Ppp2r3d	G	T	9: 101,089,179 (GRCm39)	N381K	probably benign	Het
Prrc2a	G	A	17: 35,369,018 (GRCm39)	P2006L	probably damaging	Het
Rnd2	C	T	11: 101,359,825 (GRCm39)	L57F	probably damaging	Het
Rsu1	A	G	2: 13,221,537 (GRCm39)		probably benign	Het
Selenoi	T	A	5: 30,457,740 (GRCm39)	W90R	probably damaging	Het
Spag17	T	A	3: 99,891,795 (GRCm39)	D216E	possibly damaging	Het
Spata31	C	A	13: 65,070,556 (GRCm39)	Y901*	probably null	Het
Ssrp1	T	A	2: 84,876,066 (GRCm39)	Y607*	probably null	Het
Stk10	T	A	11: 32,548,471 (GRCm39)	N346K	probably benign	Het
Surf1	G	T	2: 26,806,358 (GRCm39)		probably benign	Het
Synj2	A	T	17: 6,084,163 (GRCm39)	E283V	probably damaging	Het
Tg	G	A	15: 66,629,855 (GRCm39)		probably null	Het
Traf1	A	T	2: 34,846,289 (GRCm39)	D42E	probably benign	Het
Ttn	T	C	2: 76,571,209 (GRCm39)	I26561M	probably damaging	Het
Ubp1	T	C	9: 113,785,070 (GRCm39)	Y128H	probably damaging	Het
Vmn1r216	T	A	13: 23,283,506 (GRCm39)	I63K	probably benign	Het
Vmn1r49	T	A	6: 90,049,612 (GRCm39)	H130L	probably benign	Het
Vmn2r90	C	T	17: 17,932,567 (GRCm39)	T158I	probably damaging	Het
Vps13d	T	C	4: 144,780,725 (GRCm39)	S885G	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
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'- ACGGTTAGGTCTGGCATCTG -3'
(R):5'- CTAATCATGCACTCCTAGGATCTG -3'

Sequencing Primer
(F):5'- ATCTGTGGGCCAGTTACCTCG -3'
(R):5'- TCATGCACTCCTAGGATCTGAGAAG -3'

Posted On

2016-02-04