Mutagenetix > Incidental Mutation

Incidental Mutation 'R7468:Lca5'

578961

Institutional Source

Beutler Lab

Gene Symbol

Lca5

Ensembl Gene

ENSMUSG00000032258

Gene Name

Leber congenital amaurosis 5 (human)

Synonyms

4930431B11Rik, ORF64, 5730406O13Rik

MMRRC Submission

045542-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.454) question?

Stock #

R7468 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

83272346-83323180 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 83305509 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 99 (D99V)

Ref Sequence

ENSEMBL: ENSMUSP00000034791 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034791] [ENSMUST00000034793] [ENSMUST00000186802] [ENSMUST00000188548] [ENSMUST00000190514]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000034791
AA Change: D99V

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000034791
Gene: ENSMUSG00000032258
AA Change: D99V

Domain	Start	End	E-Value	Type
low complexity region	25	40	N/A	INTRINSIC
Pfam:Lebercilin	103	295	2.6e-66	PFAM
low complexity region	306	315	N/A	INTRINSIC
low complexity region	617	627	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000034793
AA Change: D99V

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000034793
Gene: ENSMUSG00000032258
AA Change: D99V

Domain	Start	End	E-Value	Type
low complexity region	25	40	N/A	INTRINSIC
Pfam:Lebercilin	102	295	4.8e-71	PFAM
low complexity region	306	315	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000186802
AA Change: D99V

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139529
Gene: ENSMUSG00000032258
AA Change: D99V

Domain	Start	End	E-Value	Type
low complexity region	25	40	N/A	INTRINSIC
Pfam:Lebercilin	102	176	1e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000188548

Predicted Effect

probably damaging
Transcript: ENSMUST00000190514
AA Change: D99V

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000140753
Gene: ENSMUSG00000032258
AA Change: D99V

Domain	Start	End	E-Value	Type
low complexity region	25	40	N/A	INTRINSIC
Pfam:Lebercilin	102	295	5.8e-71	PFAM
low complexity region	306	315	N/A	INTRINSIC

Coding Region Coverage

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

Validation Efficiency

98% (86/88)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is thought to be involved in centrosomal or ciliary functions. Mutations in this gene cause Leber congenital amaurosis type V. Alternatively spliced transcript variants are described. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit retinal patches of depigmentation, lack rod and cone ERG responses to light stimuli, and show loss of ciliary intraflagellar transport function in photoreceptors leading to failure of outer segment formation and photoreceptor degeneration. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abl2	T	G	1: 156,450,104 (GRCm39)	N90K	possibly damaging	Het
Acox1	T	C	11: 116,069,001 (GRCm39)	T415A	possibly damaging	Het
Acy1	T	C	9: 106,314,921 (GRCm39)	M1V	probably null	Het
Akap13	G	A	7: 75,380,213 (GRCm39)	R462H	probably damaging	Het
Alpk3	C	A	7: 80,750,746 (GRCm39)	Y1505*	probably null	Het
Ankrd17	T	C	5: 90,390,902 (GRCm39)	N2256S	probably benign	Het
Ankrd22	C	A	19: 34,126,692 (GRCm39)	C46F	possibly damaging	Het
Arhgef5	A	T	6: 43,257,605 (GRCm39)	K1291*	probably null	Het
Arl9	T	A	5: 77,158,276 (GRCm39)	Y119*	probably null	Het
Asb14	T	C	14: 26,622,805 (GRCm39)	V89A	probably benign	Het
Banp	T	G	8: 122,676,588 (GRCm39)		probably null	Het
Btn2a2	T	C	13: 23,666,933 (GRCm39)	N224S	probably benign	Het
C1ra	C	T	6: 124,499,403 (GRCm39)	Q530*	probably null	Het
C2cd6	A	C	1: 59,107,844 (GRCm39)	S273A	probably benign	Het
Cd1d2	A	T	3: 86,895,583 (GRCm39)		probably null	Het
Cdc42bpb	T	C	12: 111,306,307 (GRCm39)	D132G	probably damaging	Het
Cfap45	C	A	1: 172,362,877 (GRCm39)	Y289*	probably null	Het
Chrdl2	T	C	7: 99,659,332 (GRCm39)		probably null	Het
Cilk1	A	G	9: 78,065,221 (GRCm39)	K377R	probably benign	Het
Cst5	C	T	2: 149,247,496 (GRCm39)	L71F	probably benign	Het
Dcaf11	T	C	14: 55,802,966 (GRCm39)	F292L	possibly damaging	Het
Dgcr8	A	G	16: 18,077,487 (GRCm39)	F641S	probably damaging	Het
Dnm3	G	A	1: 162,149,198 (GRCm39)		probably null	Het
Efcab3	G	T	11: 104,640,526 (GRCm39)	S1088I	probably benign	Het
Eral1	T	C	11: 77,966,219 (GRCm39)	K320E	probably damaging	Het
Eva1a	A	G	6: 82,069,002 (GRCm39)	T110A	possibly damaging	Het
Fbxo42	A	G	4: 140,926,917 (GRCm39)	D399G	possibly damaging	Het
Frs2	T	C	10: 116,910,007 (GRCm39)	T452A	possibly damaging	Het
Git2	T	A	5: 114,871,958 (GRCm39)	D542V	probably damaging	Het
Grk2	T	A	19: 4,356,063 (GRCm39)		probably benign	Het
Gsg1l2	A	G	11: 67,676,110 (GRCm39)	N158S	possibly damaging	Het
Hc	T	C	2: 34,918,063 (GRCm39)	N740S	probably benign	Het
Hectd1	T	C	12: 51,791,588 (GRCm39)		probably null	Het
Hemk1	A	G	9: 107,208,288 (GRCm39)		probably null	Het
Hormad2	G	T	11: 4,362,245 (GRCm39)	Y126*	probably null	Het
Hr	A	G	14: 70,795,652 (GRCm39)	E399G	possibly damaging	Het
Ilf3	C	A	9: 21,314,707 (GRCm39)	H780N	unknown	Het
Inpp5e	A	T	2: 26,298,161 (GRCm39)	S147T	probably benign	Het
Irag2	C	A	6: 145,119,427 (GRCm39)		probably null	Het
Jmjd6	T	C	11: 116,733,275 (GRCm39)	D134G	probably damaging	Het
Kif23	G	T	9: 61,844,457 (GRCm39)	Y120*	probably null	Het
Klk12	T	A	7: 43,422,780 (GRCm39)	Y236N	probably damaging	Het
Kmt5b	C	A	19: 3,852,799 (GRCm39)	Y186*	probably null	Het
Krtap9-5	A	G	11: 99,840,132 (GRCm39)	T278A	unknown	Het
Leng9	A	G	7: 4,151,800 (GRCm39)	V292A	probably benign	Het
Lime1	A	G	2: 181,025,135 (GRCm39)	R231G	probably benign	Het
Mctp2	T	A	7: 71,861,438 (GRCm39)	E402D	probably damaging	Het
Mrpl28	T	A	17: 26,343,589 (GRCm39)	S116R	probably damaging	Het
Muc15	A	T	2: 110,561,862 (GRCm39)	R99S	probably benign	Het
Myh2	G	A	11: 67,083,368 (GRCm39)	A1444T	probably benign	Het
Mynn	T	A	3: 30,657,825 (GRCm39)	Y48N	probably damaging	Het
Myo1b	A	T	1: 51,836,639 (GRCm39)	V274E	possibly damaging	Het
Nemp1	T	A	10: 127,528,923 (GRCm39)	M209K	possibly damaging	Het
Nlrc4	G	T	17: 74,752,507 (GRCm39)	D625E	probably benign	Het
Or10al6	C	T	17: 38,082,910 (GRCm39)	A122V	probably damaging	Het
Or11a4	T	C	17: 37,536,276 (GRCm39)	F87L	probably benign	Het
Or4p4	T	C	2: 88,482,622 (GRCm39)	L42P	probably damaging	Het
Otog	T	C	7: 45,913,543 (GRCm39)	V792A	probably benign	Het
Paqr8	T	C	1: 21,005,442 (GRCm39)	Y199H	probably damaging	Het
Popdc3	A	G	10: 45,191,117 (GRCm39)	D76G	probably damaging	Het
Ppme1	T	C	7: 99,991,069 (GRCm39)	N210D	probably benign	Het
Prdm15	A	C	16: 97,636,842 (GRCm39)	Y158*	probably null	Het
Prrg2	A	T	7: 44,709,687 (GRCm39)	L70Q	probably benign	Het
Psmg4	C	T	13: 34,361,966 (GRCm39)	R85W	probably damaging	Het
Rab11fip4	A	T	11: 79,580,478 (GRCm39)	T437S	probably benign	Het
Rap2a	T	A	14: 120,716,338 (GRCm39)	M67K	probably damaging	Het
Rnf123	A	T	9: 107,946,208 (GRCm39)	H322Q	probably benign	Het
Rxfp2	A	T	5: 149,990,801 (GRCm39)	T521S	possibly damaging	Het
Scrn2	T	G	11: 96,923,992 (GRCm39)	V292G	possibly damaging	Het
Serpina3n	C	A	12: 104,377,656 (GRCm39)	P303H	probably benign	Het
Spop	C	T	11: 95,376,727 (GRCm39)	T260M	probably damaging	Het
Surf2	G	A	2: 26,809,354 (GRCm39)	G224D	probably benign	Het
Synm	T	G	7: 67,382,971 (GRCm39)	N669T	unknown	Het
Tmprss13	T	C	9: 45,239,721 (GRCm39)	S10P	unknown	Het
Trav9d-1	T	A	14: 53,029,970 (GRCm39)	S25T	probably benign	Het
Trpc3	A	T	3: 36,678,565 (GRCm39)	I840K	probably damaging	Het
Tsbp1	T	A	17: 34,636,539 (GRCm39)		probably null	Het
Tssc4	C	A	7: 142,622,999 (GRCm39)		probably benign	Het
Ttc39d	G	T	17: 80,523,579 (GRCm39)	R79S	possibly damaging	Het
Txlnb	T	A	10: 17,675,082 (GRCm39)	S78R	probably damaging	Het
Vmn1r142	T	A	7: 21,862,784 (GRCm39)	Q226L	possibly damaging	Het
Vmn1r230	T	C	17: 21,067,146 (GRCm39)	S112P	probably damaging	Het
Wrnip1	T	C	13: 33,000,360 (GRCm39)	F456L	possibly damaging	Het
Zc3h8	G	T	2: 128,775,215 (GRCm39)	H148Q	probably benign	Het
Zcchc3	A	G	2: 152,256,615 (GRCm39)	V28A	probably benign	Het
Zdbf2	T	A	1: 63,346,669 (GRCm39)	C1683S	probably benign	Het
Zfp874a	T	C	13: 67,573,723 (GRCm39)		probably null	Het
Zmym4	A	G	4: 126,776,029 (GRCm39)	S1260P	probably benign	Het

Other mutations in Lca5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01073:Lca5	APN	9	83,277,528 (GRCm39)	missense	probably damaging	0.98
IGL01349:Lca5	APN	9	83,308,670 (GRCm39)	missense	probably damaging	1.00
IGL01918:Lca5	APN	9	83,305,201 (GRCm39)	missense	probably damaging	1.00
IGL02035:Lca5	APN	9	83,305,365 (GRCm39)	missense	probably damaging	1.00
IGL02276:Lca5	APN	9	83,280,638 (GRCm39)	missense	possibly damaging	0.79
IGL02425:Lca5	APN	9	83,281,774 (GRCm39)	missense	probably damaging	1.00
IGL02481:Lca5	APN	9	83,305,170 (GRCm39)	missense	probably damaging	1.00
IGL02483:Lca5	APN	9	83,305,170 (GRCm39)	missense	probably damaging	1.00
R0465:Lca5	UTSW	9	83,277,920 (GRCm39)	nonsense	probably null
R0610:Lca5	UTSW	9	83,281,792 (GRCm39)	missense	probably benign	0.24
R0811:Lca5	UTSW	9	83,281,806 (GRCm39)	missense	possibly damaging	0.95
R0812:Lca5	UTSW	9	83,281,806 (GRCm39)	missense	possibly damaging	0.95
R0968:Lca5	UTSW	9	83,305,222 (GRCm39)	missense	probably benign	0.01
R1891:Lca5	UTSW	9	83,277,661 (GRCm39)	missense	probably damaging	1.00
R5223:Lca5	UTSW	9	83,280,666 (GRCm39)	missense	probably benign	0.00
R5235:Lca5	UTSW	9	83,305,107 (GRCm39)	nonsense	probably null
R5260:Lca5	UTSW	9	83,305,276 (GRCm39)	missense	probably damaging	0.98
R5531:Lca5	UTSW	9	83,280,648 (GRCm39)	missense	probably benign	0.00
R5558:Lca5	UTSW	9	83,283,796 (GRCm39)	missense	probably damaging	0.99
R5688:Lca5	UTSW	9	83,280,619 (GRCm39)	missense	probably benign	0.01
R5886:Lca5	UTSW	9	83,281,734 (GRCm39)	missense	probably benign	0.31
R6426:Lca5	UTSW	9	83,277,707 (GRCm39)	nonsense	probably null
R7108:Lca5	UTSW	9	83,305,222 (GRCm39)	missense	probably benign	0.25
R7151:Lca5	UTSW	9	83,280,693 (GRCm39)	missense	probably benign	0.20
R7314:Lca5	UTSW	9	83,277,563 (GRCm39)	missense	possibly damaging	0.86
R7378:Lca5	UTSW	9	83,277,583 (GRCm39)	missense	probably benign	0.00
R7686:Lca5	UTSW	9	83,277,292 (GRCm39)	missense	probably benign	0.00
R8874:Lca5	UTSW	9	83,277,503 (GRCm39)	missense	probably damaging	1.00
R8934:Lca5	UTSW	9	83,273,909 (GRCm39)	utr 3 prime	probably benign
R8987:Lca5	UTSW	9	83,283,796 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGAGCGCAGTAATCTCATTGTTATGG -3'
(R):5'- AGACTACTTGTTCTGGCTGGATAG -3'

Sequencing Primer
(F):5'- ATAAGTTGTGAGATCTCGTTCTCCGC -3'
(R):5'- CTGGCTGGATAGATAAATTGTAGC -3'

Posted On

2019-10-07