Mutagenetix > Incidental Mutation

Incidental Mutation 'R8008:Lrfn4'

616776

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

046048-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.433) question?

Stock #

R8008 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

4661813-4665695 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to G at 4663565 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Alanine at position 323 (G323A)

Ref Sequence

ENSEMBL: ENSMUSP00000050039 (fasta)

Gene Model

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

AlphaFold

Q80XU8

Predicted Effect

probably benign
Transcript: ENSMUST00000053597
AA Change: G323A

PolyPhen 2 Score 0.214 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000050039
Gene: ENSMUSG00000045045
AA Change: G323A

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 benign
Transcript: ENSMUST00000113822
AA Change: G323A

PolyPhen 2 Score 0.214 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000109453
Gene: ENSMUSG00000045045
AA Change: G323A

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: 99.1%

Validation Efficiency

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	A	T	13: 77,429,234 (GRCm39)	I774F	probably benign	Het
Alpi	A	G	1: 87,026,384 (GRCm39)	S536P	unknown	Het
Ankar	A	G	1: 72,705,643 (GRCm39)	V789A	possibly damaging	Het
Atp5f1b	C	A	10: 127,919,277 (GRCm39)	Q28K	unknown	Het
Brpf1	T	C	6: 113,296,050 (GRCm39)	V781A	probably benign	Het
Cd177	G	A	7: 24,451,774 (GRCm39)	S414L	not run	Het
Cimip3	T	A	17: 47,747,661 (GRCm39)	E28V	probably damaging	Het
Clca3b	T	A	3: 144,550,370 (GRCm39)	T192S	probably benign	Het
Coro2a	A	T	4: 46,551,349 (GRCm39)	S119T	probably damaging	Het
Cpped1	T	C	16: 11,646,260 (GRCm39)	N164S	probably damaging	Het
Crybg2	T	A	4: 133,818,415 (GRCm39)	N1390K	probably damaging	Het
Epn2	C	T	11: 61,437,492 (GRCm39)	A27T	probably damaging	Het
Esp34	T	C	17: 38,870,490 (GRCm39)	F128S	possibly damaging	Het
Evpl	T	A	11: 116,121,298 (GRCm39)	N410Y	probably null	Het
Flnb	A	G	14: 7,892,155 (GRCm38)	Y608C	probably damaging	Het
Fpr3	T	C	17: 18,191,715 (GRCm39)	S329P	probably benign	Het
Frem2	T	A	3: 53,560,331 (GRCm39)	N1392I	probably damaging	Het
Garin2	T	A	12: 78,761,817 (GRCm39)	D160E	probably benign	Het
Gpi1	G	T	7: 33,917,726 (GRCm39)	N249K	probably damaging	Het
Gpr87	T	C	3: 59,087,466 (GRCm39)	N13S	probably benign	Het
Gys2	T	C	6: 142,400,243 (GRCm39)	T323A	probably damaging	Het
Iqgap3	T	C	3: 88,016,770 (GRCm39)	I1084T	probably damaging	Het
Lrrc4c	A	T	2: 97,460,594 (GRCm39)	S407C	possibly damaging	Het
Map3k20	A	T	2: 72,268,613 (GRCm39)	Q540L	probably benign	Het
Myom1	T	C	17: 71,407,057 (GRCm39)	V1158A	probably benign	Het
Ncor2	T	C	5: 125,144,983 (GRCm39)	D378G	unknown	Het
Nhsl1	T	A	10: 18,284,186 (GRCm39)	D42E	probably damaging	Het
Nr0b2	C	A	4: 133,283,339 (GRCm39)	A192E	probably benign	Het
Nt5c1b	A	G	12: 10,425,000 (GRCm39)	D182G	possibly damaging	Het
Or12d14-ps1	T	C	17: 37,673,265 (GRCm39)	S86P	probably damaging	Het
Or4c115	A	T	2: 88,928,059 (GRCm39)	C71S	probably benign	Het
Or5b119	T	C	19: 13,457,170 (GRCm39)	T131A	probably benign	Het
Or5k15	T	C	16: 58,710,251 (GRCm39)	T111A	probably benign	Het
Or8b12	A	T	9: 37,658,089 (GRCm39)	I220F	probably damaging	Het
Pepd	A	G	7: 34,721,126 (GRCm39)	N250S	probably benign	Het
Plscr4	C	T	9: 92,372,843 (GRCm39)	R322*	probably null	Het
Pmp22	C	T	11: 63,049,233 (GRCm39)	R159C	probably damaging	Het
Pou3f1	C	T	4: 124,552,764 (GRCm39)	A422V	unknown	Het
Rab11fip3	A	G	17: 26,286,956 (GRCm39)	L399P	probably damaging	Het
Rragc	A	G	4: 123,829,340 (GRCm39)	D352G	probably damaging	Het
Ryr2	A	G	13: 11,671,980 (GRCm39)	V3420A	probably benign	Het
Sez6	T	A	11: 77,864,082 (GRCm39)	Y521*	probably null	Het
Smc4	T	C	3: 68,914,645 (GRCm39)	V86A	probably damaging	Het
Stap2	T	A	17: 56,304,790 (GRCm39)	M331L	probably benign	Het
Syt8	G	A	7: 141,992,259 (GRCm39)	R89H	probably benign	Het
Tcof1	G	C	18: 60,962,123 (GRCm39)	A702G	possibly damaging	Het
Trim21	G	T	7: 102,209,183 (GRCm39)	T280K	probably benign	Het
Trim36	C	A	18: 46,305,556 (GRCm39)	V476F	probably benign	Het
Troap	G	T	15: 98,973,511 (GRCm39)	R56L	probably benign	Het
Ttn	A	T	2: 76,667,130 (GRCm39)	I11492K	unknown	Het
Tuft1	T	C	3: 94,521,440 (GRCm39)	T390A	probably damaging	Het
Ucp1	T	C	8: 84,020,640 (GRCm39)	I150T	probably benign	Het
Usp17lb	A	T	7: 104,490,481 (GRCm39)	C149S	possibly damaging	Het
Vmn1r159	A	T	7: 22,542,665 (GRCm39)	N122K	possibly damaging	Het
Vmn1r237	T	C	17: 21,534,456 (GRCm39)	C60R	probably damaging	Het
Wdr12	A	T	1: 60,128,494 (GRCm39)	Y85*	probably null	Het
Wdr3	T	C	3: 100,062,252 (GRCm39)	D221G	probably benign	Het
Wdr97	G	A	15: 76,244,832 (GRCm39)	E1125K		Het
Zan	T	C	5: 137,403,624 (GRCm39)	E3974G	unknown	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
R7779:Lrfn4	UTSW	19	4,663,715 (GRCm39)	missense	probably damaging	1.00
R7968:Lrfn4	UTSW	19	4,663,343 (GRCm39)	missense	probably benign	0.06
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'- AGCAGAAGCAGCAATGTCCG -3'
(R):5'- TGCACTGCAACTGTGAGCTG -3'

Sequencing Primer
(F):5'- CCGAAGGCCCAGGACGG -3'
(R):5'- ATGACCTGGAAACCTGCG -3'

Posted On

2020-01-23