Mutagenetix > Incidental Mutation

Incidental Mutation 'R1838:Lrfn1'

205495

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

039865-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.519) question?

Stock #

R1838 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

28451980-28468242 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 28459768 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Leucine at position 371 (I371L)

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 damaging
Transcript: ENSMUST00000055110
AA Change: I371L

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000057645
Gene: ENSMUSG00000030600
AA Change: I371L

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 damaging
Transcript: ENSMUST00000108288
AA Change: I371L

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000103923
Gene: ENSMUSG00000030600
AA Change: I371L

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: I371L

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000139609
Gene: ENSMUSG00000030600
AA Change: I371L

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: 97.4%
3x: 96.9%
10x: 95.2%
20x: 92.4%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630073D07Rik	T	C	6: 132,626,727	D22G	unknown	Het
Abca4	G	A	3: 122,128,305	R1170K	probably benign	Het
Adam28	T	C	14: 68,639,210	N197S	possibly damaging	Het
Adamtsl3	G	T	7: 82,493,373	R267L	probably damaging	Het
Adgrb2	A	T	4: 130,010,231	T717S	probably benign	Het
Adgrb3	A	G	1: 25,084,270	S1417P	probably damaging	Het
Afg3l2	A	T	18: 67,414,172	V561D	probably damaging	Het
Atp13a2	T	A	4: 140,994,332	Y244*	probably null	Het
BB014433	C	G	8: 15,042,629	V75L	unknown	Het
Btnl6	T	A	17: 34,515,542	D82V	probably damaging	Het
Ccdc178	A	G	18: 22,067,638	Y421H	probably damaging	Het
Cdc123	A	T	2: 5,794,891		probably null	Het
Cdhr5	C	T	7: 141,272,603	V367I	possibly damaging	Het
Celsr3	A	G	9: 108,829,906	H1196R	probably benign	Het
Chd8	T	C	14: 52,204,883	S2077G	probably benign	Het
Col6a5	G	A	9: 105,864,833	H2296Y	probably benign	Het
Ctnna2	T	C	6: 77,845,542	D26G	probably damaging	Het
Ctr9	G	T	7: 111,052,303	R910L	possibly damaging	Het
Cyp2t4	G	T	7: 27,158,416	R455L	possibly damaging	Het
Cyp3a13	A	T	5: 137,911,632		probably null	Het
Dennd3	T	C	15: 73,565,100	S1059P	probably damaging	Het
Dennd4c	A	G	4: 86,825,178	T1135A	probably benign	Het
Dnah7b	T	C	1: 46,116,177	V295A	probably benign	Het
Dnah7b	C	A	1: 46,277,105	T3126K	probably damaging	Het
Ehbp1l1	C	T	19: 5,717,691	E1195K	probably benign	Het
Exoc6b	T	A	6: 84,853,678	I447L	probably benign	Het
Glt1d1	G	A	5: 127,678,129	V202I	probably benign	Het
Grk1	T	C	8: 13,416,155	V533A	possibly damaging	Het
Gsdma3	C	T	11: 98,629,858	A105V	probably benign	Het
Gzma	T	A	13: 113,095,984	I131F	probably damaging	Het
Helq	A	T	5: 100,771,879	L35*	probably null	Het
Hnrnpll	T	C	17: 80,038,623	N403S	probably damaging	Het
Hsf5	A	G	11: 87,636,055	K518E	probably benign	Het
Ighe	T	A	12: 113,271,850	H258L	unknown	Het
Il6ra	T	C	3: 89,890,272	D96G	probably benign	Het
Ints13	C	T	6: 146,566,611	A129T	possibly damaging	Het
Ipo7	T	A	7: 110,042,109	H345Q	probably damaging	Het
Kcna2	A	T	3: 107,104,512	E136D	probably benign	Het
Kif5a	G	A	10: 127,236,815	Q702*	probably null	Het
Klhdc7a	G	T	4: 139,967,070	P189T	probably benign	Het
Krtap4-9	A	G	11: 99,785,396		probably benign	Het
Lamc3	T	C	2: 31,925,582	S1097P	possibly damaging	Het
Ldlrad2	A	T	4: 137,572,170	N114K	probably benign	Het
Lrwd1	A	G	5: 136,132,388	V240A	probably benign	Het
Lypd1	A	T	1: 125,873,371		probably benign	Het
Magi2	A	T	5: 20,465,827	T163S	probably damaging	Het
Man2c1	A	G	9: 57,137,337	N354S	probably benign	Het
Map3k13	T	C	16: 21,914,189	Y514H	possibly damaging	Het
Med15	T	C	16: 17,653,562	D577G	probably benign	Het
Mroh4	A	T	15: 74,616,113	M320K	probably benign	Het
Ms4a10	T	A	19: 10,964,047	D186V	possibly damaging	Het
Myh7	T	C	14: 54,973,180	N1725S	possibly damaging	Het
Myo5c	A	T	9: 75,273,553	R741S	probably damaging	Het
Naip6	T	C	13: 100,316,136	D139G	probably damaging	Het
Nat6	G	A	9: 107,583,017	R37H	possibly damaging	Het
Olfr1252	A	T	2: 89,721,709	M134K	probably damaging	Het
Olfr1370	A	T	13: 21,072,425	L292*	probably null	Het
Olfr229	A	T	9: 39,909,841	I13F	possibly damaging	Het
Olfr982	A	T	9: 40,074,309	M5L	probably benign	Het
Pcdhb3	A	G	18: 37,301,317	D112G	probably benign	Het
Pdpr	C	A	8: 111,134,734	P787T	probably damaging	Het
Pgm3	C	T	9: 86,569,233	V123I	probably benign	Het
Pms1	A	C	1: 53,192,098		probably null	Het
Prl2b1	A	G	13: 27,388,566	S14P	possibly damaging	Het
Prune2	T	A	19: 17,199,878	W212R	probably damaging	Het
Rabgef1	A	G	5: 130,213,021	E422G	probably benign	Het
Ralyl	A	G	3: 14,143,412	E204G	probably damaging	Het
Rbpms2	ACTGCTGCTGCTGCTGC	ACTGCTGCTGCTGCTGCTGC	9: 65,651,666		probably benign	Het
Rbpms2	TGCCGCCGCC	TGCCGCCGCCGCC	9: 65,651,680		probably benign	Het
Rit1	C	G	3: 88,729,170	T127S	probably damaging	Het
Slc16a7	C	T	10: 125,231,198	V191M	probably damaging	Het
Slc34a2	A	T	5: 53,058,436	H63L	probably benign	Het
Smpd4	G	A	16: 17,642,302		probably null	Het
Sp3	A	G	2: 72,938,176	S748P	possibly damaging	Het
Spata31d1b	G	A	13: 59,715,857	C273Y	probably benign	Het
Spata31d1b	G	A	13: 59,717,465	R809K	probably benign	Het
Tmco5	A	T	2: 116,880,879	E90V	probably damaging	Het
Tnxb	A	T	17: 34,678,910	D844V	probably damaging	Het
Tpi1	T	C	6: 124,814,152	T41A	probably benign	Het
Ttn	T	C	2: 76,727,192	I29853V	probably damaging	Het
Vmn2r26	C	T	6: 124,024,771	T5I	probably benign	Het
Wdr95	A	G	5: 149,599,366	D663G	probably benign	Het
Zbtb39	T	C	10: 127,742,700	F381S	probably damaging	Het
Zfp523	T	A	17: 28,194,993	I34N	probably damaging	Het
Zfp646	T	A	7: 127,879,739	Y363N	probably damaging	Het
Zfp712	A	C	13: 67,042,047	C139G	probably damaging	Het
Zfp958	A	G	8: 4,628,590	H205R	probably damaging	Het
Zfp974	G	A	7: 27,910,356	P648L	possibly damaging	Het

Other mutations in Lrfn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00494:Lrfn1	APN	7	28460017	missense	probably damaging	1.00
IGL01565:Lrfn1	APN	7	28458769	missense	probably damaging	1.00
IGL01622:Lrfn1	APN	7	28466686	missense	probably damaging	1.00
IGL01623:Lrfn1	APN	7	28466686	missense	probably damaging	1.00
IGL02176:Lrfn1	APN	7	28458686	intron	probably benign
IGL02642:Lrfn1	APN	7	28458688	intron	probably benign
R1123:Lrfn1	UTSW	7	28467119	missense	possibly damaging	0.71
R3000:Lrfn1	UTSW	7	28467407	missense	probably damaging	1.00
R3551:Lrfn1	UTSW	7	28460054	missense	possibly damaging	0.90
R3905:Lrfn1	UTSW	7	28466869	missense	possibly damaging	0.49
R4246:Lrfn1	UTSW	7	28459942	missense	probably benign	0.03
R5621:Lrfn1	UTSW	7	28466836	missense	probably damaging	1.00
R6267:Lrfn1	UTSW	7	28459744	missense	probably benign	0.01
R6902:Lrfn1	UTSW	7	28459813	missense	probably benign	0.10
R7059:Lrfn1	UTSW	7	28466930	missense	possibly damaging	0.65
R7073:Lrfn1	UTSW	7	28459972	missense	possibly damaging	0.94
R7208:Lrfn1	UTSW	7	28467139	missense	probably benign
R7402:Lrfn1	UTSW	7	28459522	missense	probably damaging	1.00
R8378:Lrfn1	UTSW	7	28459732	missense	probably benign	0.26
R8791:Lrfn1	UTSW	7	28459919	missense	probably benign	0.00
R8870:Lrfn1	UTSW	7	28459493	missense	possibly damaging	0.71
R9452:Lrfn1	UTSW	7	28459732	missense	probably damaging	1.00
R9483:Lrfn1	UTSW	7	28458758	missense	probably damaging	1.00
R9579:Lrfn1	UTSW	7	28467344	missense	probably damaging	1.00
R9649:Lrfn1	UTSW	7	28466830	missense	probably damaging	1.00
Z1176:Lrfn1	UTSW	7	28459115	missense	possibly damaging	0.66

Predicted Primers

PCR Primer
(F):5'- GAGGAATTTCTATGTGAGCCCC -3'
(R):5'- GTGAGTTCAGCAGCCACAAG -3'

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

Posted On

2014-06-23