Mutagenetix > Incidental Mutation

Incidental Mutation 'R7779:Lrfn4'

599125

Institutional Source

Beutler Lab

Gene Symbol

Lrfn4

Ensembl Gene

ENSMUSG00000045045

Gene Name

leucine rich repeat and fibronectin type III domain containing 4

Synonyms

SALM3

MMRRC Submission

045835-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.479) question?

Stock #

R7779 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

4661813-4665695 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 4663715 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 273 (E273G)

Ref Sequence

ENSEMBL: ENSMUSP00000050039 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000053597] [ENSMUST00000068004] [ENSMUST00000113822] [ENSMUST00000113825] [ENSMUST00000224726]

AlphaFold

Q80XU8

Predicted Effect

probably damaging
Transcript: ENSMUST00000053597
AA Change: E273G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000050039
Gene: ENSMUSG00000045045
AA Change: E273G

Domain	Start	End	E-Value	Type
LRRNT	16	52	1.16e0	SMART
LRR	71	94	3.86e0	SMART
LRR_TYP	95	118	9.44e-2	SMART
LRR	120	142	1.23e0	SMART
LRR	144	166	1.09e1	SMART
LRR_TYP	168	191	7.37e-4	SMART
LRR	192	215	1.45e1	SMART
LRRCT	234	279	1.27e-3	SMART
IGc2	293	358	3.35e-14	SMART
FN3	403	484	1.77e-2	SMART
transmembrane domain	517	539	N/A	INTRINSIC
low complexity region	565	585	N/A	INTRINSIC
low complexity region	614	626	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000068004

SMART Domains

Protein: ENSMUSP00000063825
Gene: ENSMUSG00000024892

Domain	Start	End	E-Value	Type
low complexity region	8	22	N/A	INTRINSIC
Pfam:CPSase_L_chain	37	147	3.3e-45	PFAM
Pfam:ATP-grasp_4	149	334	3.9e-19	PFAM
Pfam:CPSase_L_D2	152	361	7.2e-77	PFAM
Pfam:Dala_Dala_lig_C	161	329	1.5e-11	PFAM
Biotin_carb_C	376	483	1.21e-50	SMART
low complexity region	513	541	N/A	INTRINSIC
Pfam:HMGL-like	564	838	8.2e-29	PFAM
Pfam:PYC_OADA	862	1062	1.4e-72	PFAM
Pfam:Biotin_lipoyl	1111	1178	1.4e-20	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000113822
AA Change: E273G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000109453
Gene: ENSMUSG00000045045
AA Change: E273G

Domain	Start	End	E-Value	Type
LRRNT	16	52	1.16e0	SMART
LRR	71	94	3.86e0	SMART
LRR_TYP	95	118	9.44e-2	SMART
LRR	120	142	1.23e0	SMART
LRR	144	166	1.09e1	SMART
LRR_TYP	168	191	7.37e-4	SMART
LRR	192	215	1.45e1	SMART
LRRCT	234	279	1.27e-3	SMART
IGc2	293	358	3.35e-14	SMART
FN3	403	484	1.77e-2	SMART
transmembrane domain	517	539	N/A	INTRINSIC
low complexity region	565	585	N/A	INTRINSIC
low complexity region	614	626	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000113825

SMART Domains

Protein: ENSMUSP00000109456
Gene: ENSMUSG00000024892

Domain	Start	End	E-Value	Type
low complexity region	7	21	N/A	INTRINSIC
Pfam:CPSase_L_chain	36	146	1.1e-43	PFAM
Pfam:ATP-grasp_4	148	332	2.9e-19	PFAM
Pfam:CPSase_L_D2	151	360	4.2e-77	PFAM
Pfam:Dala_Dala_lig_C	158	328	7.9e-13	PFAM
Biotin_carb_C	375	482	1.21e-50	SMART
low complexity region	512	540	N/A	INTRINSIC
Pfam:HMGL-like	571	821	3.4e-28	PFAM
Pfam:PYC_OADA	861	1062	3.4e-69	PFAM
Pfam:Biotin_lipoyl	1110	1177	1.8e-21	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000224726

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.2%

Validation Efficiency

98% (92/94)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele display hypoactivity and a decreased excitatory synapse number in the hippocampal CA1 region, but show normal synaptic plasticity and hippocampus-dependent learning and memory. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9330159F19Rik	T	A	10: 29,101,316 (GRCm39)	V563E	probably damaging	Het
Adra1d	A	G	2: 131,403,805 (GRCm39)	V95A	probably damaging	Het
Ak7	A	C	12: 105,708,609 (GRCm39)	I355L	probably benign	Het
Ank1	G	A	8: 23,586,763 (GRCm39)		probably null	Het
Apol7c	A	T	15: 77,409,946 (GRCm39)	H333Q	probably damaging	Het
Arfgef3	T	C	10: 18,470,771 (GRCm39)	M1665V	probably damaging	Het
Arid5b	A	G	10: 67,932,606 (GRCm39)	Y1099H	probably damaging	Het
Atp8b1	A	G	18: 64,674,453 (GRCm39)	S943P	probably damaging	Het
BC005537	C	T	13: 24,987,382 (GRCm39)	R7W	possibly damaging	Het
Bcl2l2	C	T	14: 55,121,836 (GRCm39)		probably benign	Het
Bco1	A	G	8: 117,844,135 (GRCm39)	Y283C	probably damaging	Het
Brd4	A	T	17: 32,431,910 (GRCm39)	D652E	probably benign	Het
Cacna1s	G	A	1: 136,046,767 (GRCm39)	A1799T	probably damaging	Het
Camsap3	A	G	8: 3,647,887 (GRCm39)	Y65C	probably damaging	Het
Capn1	T	C	19: 6,044,116 (GRCm39)	K535E	probably benign	Het
Cbl	A	G	9: 44,070,393 (GRCm39)	S480P	probably benign	Het
Cfap99	A	C	5: 34,469,008 (GRCm39)	N294T	probably benign	Het
Defa24	A	C	8: 22,225,355 (GRCm39)	S82R	probably benign	Het
Dnai2	T	C	11: 114,645,235 (GRCm39)	F557L	possibly damaging	Het
Dnhd1	T	A	7: 105,327,122 (GRCm39)	H690Q	probably benign	Het
Dock2	A	G	11: 34,605,282 (GRCm39)	V279A	probably benign	Het
Dst	T	A	1: 34,233,678 (GRCm39)	V3462E	probably damaging	Het
E2f3	T	G	13: 30,102,598 (GRCm39)	H221P	probably damaging	Het
Eif2b4	A	T	5: 31,347,998 (GRCm39)	I238N	probably damaging	Het
Eno4	T	C	19: 58,956,975 (GRCm39)	S530P	probably benign	Het
Epb42	T	G	2: 120,864,916 (GRCm39)	K58N	probably benign	Het
Etl4	C	T	2: 20,714,288 (GRCm39)	T129I	probably damaging	Het
Extl1	A	G	4: 134,085,014 (GRCm39)	F652S	probably damaging	Het
Extl1	T	C	4: 134,087,908 (GRCm39)	K449E	probably benign	Het
F13b	T	A	1: 139,444,124 (GRCm39)	V486E	probably benign	Het
Fbln2	T	A	6: 91,210,176 (GRCm39)	L40Q	probably damaging	Het
Glp2r	C	T	11: 67,600,609 (GRCm39)	W413*	probably null	Het
Grin2b	A	T	6: 135,755,792 (GRCm39)	Y507*	probably null	Het
H2-M11	G	T	17: 36,859,698 (GRCm39)	L230F	probably benign	Het
Il36a	T	C	2: 24,106,613 (GRCm39)	Y66H	probably damaging	Het
Itpr1	A	G	6: 108,500,309 (GRCm39)	E2634G	possibly damaging	Het
Itpr3	A	T	17: 27,315,037 (GRCm39)	Y728F	probably damaging	Het
Jak1	C	T	4: 101,017,339 (GRCm39)	E764K	probably benign	Het
Jak3	G	T	8: 72,139,932 (GRCm39)	R1045L	probably benign	Het
Jam2	T	C	16: 84,606,271 (GRCm39)	I95T	probably damaging	Het
Kdf1	T	C	4: 133,255,796 (GRCm39)	V171A	probably damaging	Het
Lactbl1	A	T	4: 136,358,307 (GRCm39)	K93*	probably null	Het
Lcn6	T	C	2: 25,570,805 (GRCm39)	V131A	probably benign	Het
Lpar5	T	A	6: 125,059,207 (GRCm39)	D309E	probably damaging	Het
Lta4h	C	T	10: 93,310,811 (GRCm39)	T447I	probably benign	Het
Lyst	A	G	13: 13,809,128 (GRCm39)	E266G	probably damaging	Het
Mab21l1	A	T	3: 55,690,796 (GRCm39)	I128F	possibly damaging	Het
Mrgprb4	T	G	7: 47,848,895 (GRCm39)	N11T	probably benign	Het
Mroh6	G	A	15: 75,760,505 (GRCm39)	T23I	possibly damaging	Het
Myo1f	T	C	17: 33,797,247 (GRCm39)	I143T	probably benign	Het
Myof	C	T	19: 37,927,838 (GRCm39)	D1092N	probably damaging	Het
Ncan	G	T	8: 70,567,661 (GRCm39)	D150E	probably damaging	Het
Or1d2	T	A	11: 74,255,771 (GRCm39)	I92N	probably damaging	Het
Or2y1f	T	A	11: 49,185,048 (GRCm39)	L300Q	probably damaging	Het
Or6c88	A	T	10: 129,407,180 (GRCm39)	I219F	probably damaging	Het
Pcm1	A	G	8: 41,782,061 (GRCm39)	Y1948C	probably damaging	Het
Pcsk6	A	T	7: 65,675,152 (GRCm39)	T669S	probably benign	Het
Pdlim5	A	C	3: 141,948,447 (GRCm39)	N613K	probably benign	Het
Pdzk1	T	A	3: 96,764,589 (GRCm39)	V291D	probably damaging	Het
Plbd2	T	C	5: 120,625,743 (GRCm39)	Q408R	probably damaging	Het
Ppp1r37	C	A	7: 19,266,712 (GRCm39)	A392S	possibly damaging	Het
Proser2	T	A	2: 6,107,878 (GRCm39)		probably null	Het
Psmd12	T	C	11: 107,388,405 (GRCm39)	V406A	probably benign	Het
Rab3gap2	T	C	1: 184,991,641 (GRCm39)	V709A	probably damaging	Het
Radil	T	C	5: 142,473,320 (GRCm39)	E787G	probably benign	Het
Rai14	A	C	15: 10,593,112 (GRCm39)	D177E	probably damaging	Het
Rbms2	G	A	10: 127,979,315 (GRCm39)	T166I	probably damaging	Het
Rrh	C	T	3: 129,608,969 (GRCm39)	C115Y	probably benign	Het
Slc1a6	C	T	10: 78,631,789 (GRCm39)	T205I	probably damaging	Het
Sost	T	C	11: 101,857,675 (GRCm39)	E42G	possibly damaging	Het
Spcs3	T	A	8: 54,982,805 (GRCm39)	I46F	possibly damaging	Het
Spg11	A	G	2: 121,901,420 (GRCm39)	S1507P	probably damaging	Het
Sprtn	C	T	8: 125,624,982 (GRCm39)	P29L	possibly damaging	Het
Sptan1	C	T	2: 29,911,319 (GRCm39)	T1886I	probably damaging	Het
Strn4	T	C	7: 16,565,417 (GRCm39)	F394S	probably damaging	Het
Syt14	A	T	1: 192,666,751 (GRCm39)	M51K	unknown	Het
Terb2	A	G	2: 122,016,975 (GRCm39)	K32R	probably benign	Het
Tex15	G	A	8: 34,065,309 (GRCm39)	G1580R	probably damaging	Het
Thumpd3	T	C	6: 113,036,950 (GRCm39)	V283A	probably damaging	Het
Tm7sf2	T	C	19: 6,112,947 (GRCm39)	Y418C	possibly damaging	Het
Trim24	T	G	6: 37,896,332 (GRCm39)	F263C	probably damaging	Het
Trim24	T	A	6: 37,896,333 (GRCm39)	F263L	probably damaging	Het
Trip11	A	G	12: 101,849,796 (GRCm39)	S1423P	probably damaging	Het
Vps13c	G	A	9: 67,788,704 (GRCm39)	V326M	probably damaging	Het
Vps37c	T	C	19: 10,689,988 (GRCm39)	V150A	probably damaging	Het
Wdr90	C	T	17: 26,065,300 (GRCm39)	R1652Q	probably damaging	Het
Wfdc9	A	G	2: 164,492,516 (GRCm39)	V37A	probably damaging	Het
Yif1b	T	A	7: 28,945,328 (GRCm39)	M227K	probably damaging	Het
Zbtb18	T	C	1: 177,274,505 (GRCm39)		probably benign	Het
Zfp318	A	G	17: 46,710,820 (GRCm39)	T848A	probably benign	Het
Zfp808	T	A	13: 62,320,571 (GRCm39)	I600K	possibly damaging	Het
Zmym1	C	A	4: 126,948,038 (GRCm39)	S111I	probably benign	Het
Zmym2	A	G	14: 57,165,740 (GRCm39)	T688A	probably damaging	Het

Other mutations in Lrfn4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0715:Lrfn4	UTSW	19	4,662,668 (GRCm39)	critical splice acceptor site	probably null
R1103:Lrfn4	UTSW	19	4,663,299 (GRCm39)	missense	probably benign	0.00
R1629:Lrfn4	UTSW	19	4,663,523 (GRCm39)	missense	possibly damaging	0.60
R4406:Lrfn4	UTSW	19	4,663,299 (GRCm39)	missense	probably benign	0.00
R4459:Lrfn4	UTSW	19	4,662,662 (GRCm39)	missense	probably benign
R5543:Lrfn4	UTSW	19	4,662,191 (GRCm39)	missense	probably benign	0.41
R6115:Lrfn4	UTSW	19	4,663,937 (GRCm39)	missense	probably damaging	1.00
R6554:Lrfn4	UTSW	19	4,663,914 (GRCm39)	missense	probably damaging	0.98
R7626:Lrfn4	UTSW	19	4,663,679 (GRCm39)	missense	probably damaging	1.00
R7968:Lrfn4	UTSW	19	4,663,343 (GRCm39)	missense	probably benign	0.06
R8008:Lrfn4	UTSW	19	4,663,565 (GRCm39)	missense	probably benign	0.21
R8356:Lrfn4	UTSW	19	4,662,256 (GRCm39)	missense	probably benign	0.44
R8482:Lrfn4	UTSW	19	4,664,333 (GRCm39)	missense	probably damaging	1.00
R9180:Lrfn4	UTSW	19	4,663,353 (GRCm39)	missense	probably benign	0.01
R9507:Lrfn4	UTSW	19	4,664,357 (GRCm39)	missense	probably damaging	1.00
R9520:Lrfn4	UTSW	19	4,664,237 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CCCAATCTCTAGGGTCCCATTG -3'
(R):5'- TCTTTGCTCAGCTCAGCCAG -3'

Sequencing Primer
(F):5'- GAGAAGAGTTGCCAACCA -3'
(R):5'- ACCCTGGCACCTGATCC -3'

Posted On

2019-11-26