Mutagenetix > Incidental Mutation

Incidental Mutation 'R6267:Lrfn1'

507070

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

044405-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.405) question?

Stock #

R6267 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

28151405-28167667 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 28159169 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 363 (R363G)

Ref Sequence

ENSEMBL: ENSMUSP00000139609 (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 benign
Transcript: ENSMUST00000055110
AA Change: R363G

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000057645
Gene: ENSMUSG00000030600
AA Change: R363G

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: ENSMUST00000108288
AA Change: R363G

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000103923
Gene: ENSMUSG00000030600
AA Change: R363G

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 benign
Transcript: ENSMUST00000189877
AA Change: R363G

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000139609
Gene: ENSMUSG00000030600
AA Change: R363G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000191267

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.4%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427D14Rik	T	C	11: 72,086,580 (GRCm39)	K277R	probably damaging	Het
Aatf	T	C	11: 84,363,926 (GRCm39)	Y267C	probably benign	Het
Abi3bp	A	G	16: 56,414,860 (GRCm39)	T341A	probably damaging	Het
Acer2	T	C	4: 86,792,823 (GRCm39)	F33S	probably damaging	Het
Actr1b	A	G	1: 36,740,244 (GRCm39)	V299A	possibly damaging	Het
Ampd3	T	A	7: 110,390,387 (GRCm39)		probably null	Het
Atm	A	C	9: 53,355,300 (GRCm39)	I2898R	probably damaging	Het
Bpifb6	G	C	2: 153,748,812 (GRCm39)	K269N	possibly damaging	Het
Cacna1c	T	C	6: 118,575,684 (GRCm39)	E1927G	possibly damaging	Het
Cacna1c	T	A	6: 118,629,675 (GRCm39)	T1249S	probably benign	Het
Cars2	TCCCC	TCCC	8: 11,579,599 (GRCm39)		probably null	Het
Cbll1	A	G	12: 31,537,507 (GRCm39)	V415A	probably benign	Het
Cd300lf	C	T	11: 115,015,195 (GRCm39)	V132I	probably benign	Het
Chd2	T	C	7: 73,113,419 (GRCm39)	E1187G	probably damaging	Het
Cntrl	T	C	2: 35,019,805 (GRCm39)	L544P	probably damaging	Het
Cryga	A	C	1: 65,142,169 (GRCm39)	S75A	probably benign	Het
Dcbld1	T	A	10: 52,195,576 (GRCm39)	Y261*	probably null	Het
Ddx11	G	A	17: 66,457,724 (GRCm39)		probably null	Het
Dgke	C	T	11: 88,931,575 (GRCm39)	V560I	probably benign	Het
Dst	A	C	1: 34,267,753 (GRCm39)	D5065A	probably damaging	Het
Dusp16	C	A	6: 134,697,456 (GRCm39)		probably null	Het
Eif4enif1	T	A	11: 3,177,793 (GRCm39)	V395E	probably damaging	Het
Enox1	A	G	14: 77,815,204 (GRCm39)	T121A	probably damaging	Het
Enpp4	G	T	17: 44,413,371 (GRCm39)	N54K	probably benign	Het
Erc2	A	T	14: 27,802,112 (GRCm39)	K764M	probably damaging	Het
Ercc6	G	T	14: 32,248,360 (GRCm39)	E304*	probably null	Het
Fam117a	T	A	11: 95,254,971 (GRCm39)	C115S	possibly damaging	Het
Fcrl5	G	A	3: 87,355,631 (GRCm39)	G448E	probably damaging	Het
Galntl5	T	C	5: 25,391,163 (GRCm39)	S21P	probably benign	Het
Garnl3	T	C	2: 32,994,892 (GRCm39)	D39G	probably benign	Het
Gm14295	C	T	2: 176,500,782 (GRCm39)	Q91*	probably null	Het
Grb10	T	A	11: 11,920,639 (GRCm39)		probably benign	Het
Grip1	C	T	10: 119,911,369 (GRCm39)	Q696*	probably null	Het
Herc2	T	A	7: 55,802,914 (GRCm39)	C2112*	probably null	Het
Herc2	T	G	7: 55,854,466 (GRCm39)	L3797R	possibly damaging	Het
Ighm	T	C	12: 113,385,187 (GRCm39)	I258V	unknown	Het
Jarid2	T	A	13: 45,056,539 (GRCm39)	Y443N	possibly damaging	Het
Kif13b	A	G	14: 64,976,083 (GRCm39)	Y466C	probably damaging	Het
Krtap4-6	T	A	11: 99,556,245 (GRCm39)	R161*	probably null	Het
Lingo4	G	A	3: 94,310,697 (GRCm39)	G545E	probably benign	Het
Lmo2	T	G	2: 103,800,946 (GRCm39)	V39G	possibly damaging	Het
Loricrin	C	A	3: 91,989,119 (GRCm39)	G56*	probably null	Het
Lrp1b	T	C	2: 40,547,537 (GRCm39)	D446G	probably benign	Het
Ltbp1	G	T	17: 75,312,984 (GRCm39)	G35V	possibly damaging	Het
Magel2	G	A	7: 62,028,427 (GRCm39)	V444M	probably damaging	Het
Mkx	A	T	18: 7,000,591 (GRCm39)		probably null	Het
Ms4a7	A	T	19: 11,310,659 (GRCm39)	I20N	possibly damaging	Het
Myo5b	A	G	18: 74,750,062 (GRCm39)	Y173C	probably damaging	Het
Nek1	C	T	8: 61,525,343 (GRCm39)	Q594*	probably null	Het
Nipbl	T	C	15: 8,330,379 (GRCm39)	M2349V	possibly damaging	Het
Nmnat2	A	T	1: 152,952,717 (GRCm39)	H102L	probably damaging	Het
Nup155	T	A	15: 8,182,639 (GRCm39)	C1201S	probably damaging	Het
Or2y8	C	A	11: 52,035,423 (GRCm39)	R311S	probably benign	Het
Or4a76	G	A	2: 89,460,975 (GRCm39)	T89I	probably damaging	Het
Or52x1	G	A	7: 104,852,599 (GRCm39)	T317I	probably damaging	Het
Osbpl1a	A	G	18: 12,952,560 (GRCm39)		probably null	Het
Pcnt	A	G	10: 76,221,632 (GRCm39)	V1998A	probably benign	Het
Pitpnc1	T	C	11: 107,117,092 (GRCm39)	H193R	probably damaging	Het
Pitpnm1	T	C	19: 4,160,522 (GRCm39)	L781P	probably damaging	Het
Prdm14	A	T	1: 13,189,160 (GRCm39)	C395S	probably damaging	Het
Prmt8	A	G	6: 127,688,767 (GRCm39)	I201T	probably damaging	Het
Pter	T	C	2: 12,983,352 (GRCm39)	V119A	probably damaging	Het
Rab11fip4	T	C	11: 79,581,655 (GRCm39)		probably null	Het
Rgs9	T	C	11: 109,159,813 (GRCm39)	N173S	probably benign	Het
Rorb	C	A	19: 18,955,221 (GRCm39)	V47L	possibly damaging	Het
Rtn4r	A	G	16: 17,969,046 (GRCm39)	Y158C	probably damaging	Het
Sdr16c5	C	T	4: 4,016,162 (GRCm39)	G88E	probably damaging	Het
Sfxn1	C	T	13: 54,247,899 (GRCm39)	T208I	probably benign	Het
Sgo2b	C	T	8: 64,380,827 (GRCm39)	M668I	probably benign	Het
Slc52a3	G	T	2: 151,849,529 (GRCm39)		probably null	Het
Smco1	A	T	16: 32,092,832 (GRCm39)	M168L	probably benign	Het
Spata31d1d	G	A	13: 59,876,278 (GRCm39)	T419I	possibly damaging	Het
Spata31d1e	T	C	13: 59,890,497 (GRCm39)	D441G	probably benign	Het
Spink5	T	C	18: 44,147,824 (GRCm39)	S857P	probably damaging	Het
Stk35	T	A	2: 129,652,808 (GRCm39)	Y436*	probably null	Het
Tmem225	T	A	9: 40,059,731 (GRCm39)	I37N	probably damaging	Het
Unkl	T	C	17: 25,450,839 (GRCm39)	*232R	probably null	Het
Usp16	A	G	16: 87,280,079 (GRCm39)	N813S	probably benign	Het
Vmn1r128	A	T	7: 21,084,221 (GRCm39)	*308C	probably null	Het
Vmn2r45	A	G	7: 8,475,207 (GRCm39)	V607A	probably benign	Het
Vmn2r63	A	T	7: 42,578,059 (GRCm39)		probably null	Het
Wnk4	A	T	11: 101,164,824 (GRCm39)	N718Y	probably damaging	Het
Zfp503	G	C	14: 22,035,868 (GRCm39)	Y349*	probably null	Het
Zfp990	T	A	4: 145,264,673 (GRCm39)	F557Y	possibly 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
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
R7073:Lrfn1	UTSW	7	28,159,397 (GRCm39)	missense	possibly damaging	0.94
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'- AGGAGGAATTTCTATGTGAGCCC -3'
(R):5'- ACTGGTTGAGTCGTTGGCAC -3'

Sequencing Primer
(F):5'- TCATCACACGGCAAGCAGG -3'
(R):5'- TGAGTCGTTGGCACCAGGTC -3'

Posted On

2018-03-15