Mutagenetix > Incidental Mutation

Incidental Mutation 'R7073:Lrfn1'

549034

Institutional Source

Beutler Lab

Gene Symbol

Lrfn1

Ensembl Gene

ENSMUSG00000030600

Gene Name

leucine rich repeat and fibronectin type III domain containing 1

Synonyms

SALM2

MMRRC Submission

045169-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.342) question?

Stock #

R7073 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

28151405-28167667 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 28159397 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Phenylalanine at position 439 (L439F)

Ref Sequence

ENSEMBL: ENSMUSP00000103923 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040531] [ENSMUST00000055110] [ENSMUST00000108288] [ENSMUST00000189877] [ENSMUST00000190954]

AlphaFold

Q2WF71

Predicted Effect

probably benign
Transcript: ENSMUST00000040531

SMART Domains

Protein: ENSMUSP00000040486
Gene: ENSMUSG00000109336

Domain	Start	End	E-Value	Type
low complexity region	81	90	N/A	INTRINSIC
low complexity region	174	190	N/A	INTRINSIC
low complexity region	200	211	N/A	INTRINSIC
low complexity region	278	290	N/A	INTRINSIC
SAM	296	359	1.02e-9	SMART
low complexity region	406	420	N/A	INTRINSIC
low complexity region	433	461	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000055110
AA Change: L439F

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000057645
Gene: ENSMUSG00000030600
AA Change: L439F

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
LRR	88	111	8.67e-1	SMART
LRR	112	135	4.57e0	SMART
LRR_TYP	136	159	1.69e-3	SMART
LRR	161	184	2.54e1	SMART
LRR	185	208	2.32e-1	SMART
LRR	209	233	3.75e0	SMART
LRRCT	252	297	1.36e-3	SMART
IGc2	312	377	1.51e-12	SMART
low complexity region	389	403	N/A	INTRINSIC
low complexity region	460	471	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000108288
AA Change: L439F

PolyPhen 2 Score 0.942 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000103923
Gene: ENSMUSG00000030600
AA Change: L439F

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
LRR	88	111	8.67e-1	SMART
LRR	112	135	4.57e0	SMART
LRR_TYP	136	159	1.69e-3	SMART
LRR	161	184	2.54e1	SMART
LRR	185	208	2.32e-1	SMART
LRR	209	233	3.75e0	SMART
LRRCT	252	297	1.36e-3	SMART
IGc2	312	377	1.51e-12	SMART
low complexity region	389	403	N/A	INTRINSIC
FN3	422	502	2.68e-2	SMART
transmembrane domain	535	557	N/A	INTRINSIC
low complexity region	589	601	N/A	INTRINSIC
low complexity region	609	625	N/A	INTRINSIC
low complexity region	716	725	N/A	INTRINSIC
low complexity region	730	747	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000189877
AA Change: L439F

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000139609
Gene: ENSMUSG00000030600
AA Change: L439F

Domain	Start	End	E-Value	Type
low complexity region	2	28	N/A	INTRINSIC
LRR	88	111	8.67e-1	SMART
LRR	112	135	4.57e0	SMART
LRR_TYP	136	159	1.69e-3	SMART
LRR	161	184	2.54e1	SMART
LRR	185	208	2.32e-1	SMART
LRR	209	233	3.75e0	SMART
LRRCT	252	297	1.36e-3	SMART
IGc2	312	377	1.51e-12	SMART
low complexity region	389	403	N/A	INTRINSIC
low complexity region	460	471	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000190954

SMART Domains

Protein: ENSMUSP00000140537
Gene: ENSMUSG00000030600

Domain	Start	End	E-Value	Type
signal peptide	1	31	N/A	INTRINSIC
Blast:LRRNT	33	69	2e-18	BLAST
LRR	88	111	3.7e-3	SMART
LRR	112	135	1.9e-2	SMART
LRR_TYP	136	159	7.1e-6	SMART
LRR	161	184	1.1e-1	SMART
LRR	185	208	1e-3	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrv1	T	G	13: 81,709,593 (GRCm39)	E1133D	probably damaging	Het
Ankrd13b	A	T	11: 77,363,335 (GRCm39)	D505E	probably benign	Het
Ano1	C	T	7: 144,192,289 (GRCm39)	E361K	probably damaging	Het
Arap3	T	A	18: 38,107,495 (GRCm39)	K1341*	probably null	Het
Arhgef17	A	C	7: 100,579,198 (GRCm39)	Y583*	probably null	Het
Ash1l	G	A	3: 88,892,647 (GRCm39)	E1509K	probably damaging	Het
B430305J03Rik	T	G	3: 61,271,681 (GRCm39)	R21S	unknown	Het
Bbof1	A	G	12: 84,473,609 (GRCm39)	E313G	probably damaging	Het
Catsperb	C	T	12: 101,475,497 (GRCm39)	T347I	probably benign	Het
Ccdc24	G	T	4: 117,729,201 (GRCm39)	A92D	probably damaging	Het
Ccdc63	T	C	5: 122,249,073 (GRCm39)	T419A	probably benign	Het
Ccdc7a	C	T	8: 129,618,866 (GRCm39)	V893I	possibly damaging	Het
Ccdc88b	G	T	19: 6,831,330 (GRCm39)	D537E	probably benign	Het
Cd276	T	C	9: 58,444,615 (GRCm39)	S119G	probably damaging	Het
Cdkn3	T	C	14: 47,004,647 (GRCm39)	Y70H	possibly damaging	Het
Cdo1	G	A	18: 46,861,266 (GRCm39)		probably benign	Het
Cdr2	A	T	7: 120,581,247 (GRCm39)	F10Y	probably damaging	Het
Cep290	A	T	10: 100,374,865 (GRCm39)	K1370N	possibly damaging	Het
Crb1	T	A	1: 139,176,049 (GRCm39)	I645F	probably damaging	Het
Cul7	T	C	17: 46,969,657 (GRCm39)	W975R	probably damaging	Het
Ddx39b	A	C	17: 35,471,826 (GRCm39)	E324A	probably benign	Het
Diaph1	T	G	18: 38,022,867 (GRCm39)		probably null	Het
Dnah2	G	A	11: 69,321,318 (GRCm39)	R3917*	probably null	Het
Dnph1	T	A	17: 46,807,815 (GRCm39)	L27Q	probably damaging	Het
Duox2	A	G	2: 122,119,788 (GRCm39)	F880S	probably damaging	Het
Ell2	C	A	13: 75,910,006 (GRCm39)	L119M	probably damaging	Het
Enpep	A	T	3: 129,106,319 (GRCm39)	Y302*	probably null	Het
Ergic2	G	T	6: 148,096,707 (GRCm39)	H186Q	probably damaging	Het
Fam83b	T	C	9: 76,453,031 (GRCm39)	D12G	probably benign	Het
Fbxw16	A	T	9: 109,270,123 (GRCm39)	V206D	probably damaging	Het
Fhod1	A	T	8: 106,063,771 (GRCm39)	V278D	unknown	Het
Gba2	G	C	4: 43,573,753 (GRCm39)	Q180E	probably damaging	Het
Grhl3	G	A	4: 135,300,723 (GRCm39)	L5F	probably benign	Het
H2-T15	A	T	17: 36,369,235 (GRCm39)	C7S	unknown	Het
Ifit1bl1	C	T	19: 34,576,667 (GRCm39)		probably null	Het
Ift57	A	G	16: 49,584,230 (GRCm39)	T413A	probably benign	Het
Itga2	A	G	13: 114,996,149 (GRCm39)	F714S	probably damaging	Het
Jmy	A	G	13: 93,577,841 (GRCm39)	S776P	probably benign	Het
Kbtbd8	G	A	6: 95,098,814 (GRCm39)	A108T	probably damaging	Het
Kpna6	G	A	4: 129,548,139 (GRCm39)	A230V	probably damaging	Het
Lrrc1	T	A	9: 77,375,847 (GRCm39)	I147F	probably benign	Het
Lrrc7	C	T	3: 157,832,884 (GRCm39)	G1425R	probably damaging	Het
Madd	T	A	2: 90,992,854 (GRCm39)	I1022F	probably damaging	Het
Map2k2	A	T	10: 80,942,017 (GRCm39)	T13S	probably benign	Het
Mdc1	G	A	17: 36,164,960 (GRCm39)	V1459I	probably benign	Het
Mdh1b	G	A	1: 63,760,719 (GRCm39)	T114M	probably damaging	Het
Mfsd2a	T	C	4: 122,845,088 (GRCm39)	I208V	possibly damaging	Het
Mmrn1	T	A	6: 60,965,411 (GRCm39)	D1147E	probably damaging	Het
Nbeal2	T	A	9: 110,455,177 (GRCm39)	I2574F	probably damaging	Het
Nr1d1	T	G	11: 98,662,892 (GRCm39)	S34R	probably damaging	Het
Nr3c1	A	T	18: 39,619,449 (GRCm39)	D279E	probably benign	Het
Nrde2	T	C	12: 100,098,747 (GRCm39)	D640G	probably benign	Het
Odf4	A	G	11: 68,817,514 (GRCm39)	L58P	probably damaging	Het
Or4k41	A	T	2: 111,279,631 (GRCm39)	I49F	probably benign	Het
Or4p22	A	T	2: 88,317,651 (GRCm39)	I192F	probably benign	Het
Otud6b	A	C	4: 14,811,743 (GRCm39)	M300R	probably damaging	Het
Pamr1	T	A	2: 102,471,280 (GRCm39)	D534E	probably benign	Het
Pcdh7	T	A	5: 57,878,299 (GRCm39)	V618E	probably benign	Het
Pcgf6	A	C	19: 47,031,226 (GRCm39)	N266K	possibly damaging	Het
Plcz1	A	T	6: 139,968,849 (GRCm39)	Y196*	probably null	Het
Plxna1	A	T	6: 89,334,311 (GRCm39)	L106Q	probably damaging	Het
Qrich2	G	A	11: 116,337,701 (GRCm39)	A184V	probably damaging	Het
Rimkla	A	G	4: 119,325,275 (GRCm39)	L378S	probably benign	Het
Rufy1	G	T	11: 50,295,290 (GRCm39)	H472Q	probably benign	Het
Samd7	T	A	3: 30,810,631 (GRCm39)	M216K	probably benign	Het
Samd9l	A	T	6: 3,375,856 (GRCm39)	Y468*	probably null	Het
Scn2a	T	G	2: 65,558,787 (GRCm39)	L1194R	probably benign	Het
Sgo2a	T	A	1: 58,056,944 (GRCm39)	S1043T	possibly damaging	Het
Slc6a17	G	T	3: 107,378,755 (GRCm39)	H642Q	probably benign	Het
Smox	C	T	2: 131,364,031 (GRCm39)	A45V	possibly damaging	Het
St6galnac3	T	A	3: 153,117,274 (GRCm39)	T150S	possibly damaging	Het
Strip2	T	A	6: 29,941,911 (GRCm39)	I627N	possibly damaging	Het
Sv2c	A	T	13: 96,224,758 (GRCm39)	C184S	probably damaging	Het
Tm7sf2	A	T	19: 6,116,527 (GRCm39)		probably null	Het
Ttc28	T	C	5: 111,371,282 (GRCm39)	I608T	possibly damaging	Het
Vmn1r183	T	G	7: 23,754,926 (GRCm39)	L243R	probably damaging	Het
Vmn1r68	T	C	7: 10,261,778 (GRCm39)	T107A	probably benign	Het
Vnn3	G	A	10: 23,740,311 (GRCm39)	G205R	probably damaging	Het
Zfp516	T	A	18: 83,006,325 (GRCm39)		probably null	Het
Zpbp2	A	G	11: 98,443,335 (GRCm39)	D56G	probably damaging	Het

Other mutations in Lrfn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00494:Lrfn1	APN	7	28,159,442 (GRCm39)	missense	probably damaging	1.00
IGL01565:Lrfn1	APN	7	28,158,194 (GRCm39)	missense	probably damaging	1.00
IGL01622:Lrfn1	APN	7	28,166,111 (GRCm39)	missense	probably damaging	1.00
IGL01623:Lrfn1	APN	7	28,166,111 (GRCm39)	missense	probably damaging	1.00
IGL02176:Lrfn1	APN	7	28,158,111 (GRCm39)	intron	probably benign
IGL02642:Lrfn1	APN	7	28,158,113 (GRCm39)	intron	probably benign
R1123:Lrfn1	UTSW	7	28,166,544 (GRCm39)	missense	possibly damaging	0.71
R1838:Lrfn1	UTSW	7	28,159,193 (GRCm39)	missense	probably damaging	0.98
R3000:Lrfn1	UTSW	7	28,166,832 (GRCm39)	missense	probably damaging	1.00
R3551:Lrfn1	UTSW	7	28,159,479 (GRCm39)	missense	possibly damaging	0.90
R3905:Lrfn1	UTSW	7	28,166,294 (GRCm39)	missense	possibly damaging	0.49
R4246:Lrfn1	UTSW	7	28,159,367 (GRCm39)	missense	probably benign	0.03
R5621:Lrfn1	UTSW	7	28,166,261 (GRCm39)	missense	probably damaging	1.00
R6267:Lrfn1	UTSW	7	28,159,169 (GRCm39)	missense	probably benign	0.01
R6902:Lrfn1	UTSW	7	28,159,238 (GRCm39)	missense	probably benign	0.10
R7059:Lrfn1	UTSW	7	28,166,355 (GRCm39)	missense	possibly damaging	0.65
R7208:Lrfn1	UTSW	7	28,166,564 (GRCm39)	missense	probably benign
R7402:Lrfn1	UTSW	7	28,158,947 (GRCm39)	missense	probably damaging	1.00
R8378:Lrfn1	UTSW	7	28,159,157 (GRCm39)	missense	probably benign	0.26
R8791:Lrfn1	UTSW	7	28,159,344 (GRCm39)	missense	probably benign	0.00
R8870:Lrfn1	UTSW	7	28,158,918 (GRCm39)	missense	possibly damaging	0.71
R9452:Lrfn1	UTSW	7	28,159,157 (GRCm39)	missense	probably damaging	1.00
R9483:Lrfn1	UTSW	7	28,158,183 (GRCm39)	missense	probably damaging	1.00
R9579:Lrfn1	UTSW	7	28,166,769 (GRCm39)	missense	probably damaging	1.00
R9649:Lrfn1	UTSW	7	28,166,255 (GRCm39)	missense	probably damaging	1.00
Z1176:Lrfn1	UTSW	7	28,158,540 (GRCm39)	missense	possibly damaging	0.66

Predicted Primers

PCR Primer
(F):5'- TGCATAGCCTCCAATGCTGC -3'
(R):5'- TACAGGCCTATCCAGAGCTG -3'

Sequencing Primer
(F):5'- TCCAATGCTGCGGGGGAAG -3'
(R):5'- AGCTGGAACTAAGCAAGGTC -3'

Posted On

2019-05-15