Mutagenetix > Incidental Mutation

Incidental Mutation 'R4406:Lrfn4'

327681

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

041688-MU

Accession Numbers

Essential gene?

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

Stock #

R4406 (G1)

Quality Score

202

Status

Validated

Chromosome

Chromosomal Location

4661813-4665695 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 4663299 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 412 (T412A)

Ref Sequence

ENSEMBL: ENSMUSP00000109453 (fasta)

Gene Model

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

AlphaFold

Q80XU8

Predicted Effect

probably benign
Transcript: ENSMUST00000053597
AA Change: T412A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000050039
Gene: ENSMUSG00000045045
AA Change: T412A

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: T412A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000109453
Gene: ENSMUSG00000045045
AA Change: T412A

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

Meta Mutation Damage Score

0.0623

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

100% (45/45)

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: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	C	T	11: 84,171,275 (GRCm39)	L1170F	probably benign	Het
Acss3	A	T	10: 106,889,198 (GRCm39)	D207E	probably damaging	Het
Adgrl1	T	C	8: 84,656,671 (GRCm39)	S325P	probably damaging	Het
Ankrd37	A	G	8: 46,450,131 (GRCm39)		probably benign	Het
Atp13a2	C	T	4: 140,733,787 (GRCm39)	P1059S	probably damaging	Het
Camkv	T	C	9: 107,823,418 (GRCm39)		probably null	Het
Ces1f	T	C	8: 93,989,950 (GRCm39)	T387A	probably benign	Het
Dmxl1	T	A	18: 50,022,620 (GRCm39)	L1653I	probably damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Fat2	G	A	11: 55,153,094 (GRCm39)	A3706V	probably benign	Het
Fbln1	T	A	15: 85,115,757 (GRCm39)		probably null	Het
Gm1527	G	A	3: 28,949,874 (GRCm39)	V45M	possibly damaging	Het
Gm5084	A	G	13: 60,360,380 (GRCm39)		noncoding transcript	Het
Itpr1	T	A	6: 108,331,624 (GRCm39)	H194Q	probably damaging	Het
Kif24	A	T	4: 41,393,954 (GRCm39)	L973Q	probably damaging	Het
Ly75	T	C	2: 60,184,894 (GRCm39)	E420G	probably damaging	Het
Map3k12	T	C	15: 102,413,837 (GRCm39)	T45A	probably damaging	Het
Mib1	A	C	18: 10,763,289 (GRCm39)	K446N	probably damaging	Het
Mrpl4	T	C	9: 20,918,231 (GRCm39)	W146R	probably damaging	Het
Myof	A	G	19: 37,911,426 (GRCm39)	S1502P	probably damaging	Het
Nomo1	A	G	7: 45,706,092 (GRCm39)	N482S	probably benign	Het
Or2y1	G	A	11: 49,385,744 (GRCm39)	R128H	probably benign	Het
Or5b105	A	G	19: 13,079,958 (GRCm39)	S237P	possibly damaging	Het
Or5b96	A	T	19: 12,867,598 (GRCm39)	Y114*	probably null	Het
Or8g21	T	C	9: 38,905,865 (GRCm39)	I289V	possibly damaging	Het
Or9s15	T	A	1: 92,525,036 (GRCm39)	M265K	possibly damaging	Het
Osbpl10	C	T	9: 114,938,549 (GRCm39)	H70Y	probably damaging	Het
Pdilt	A	C	7: 119,094,232 (GRCm39)	S340A	probably damaging	Het
Ppan	C	A	9: 20,802,288 (GRCm39)	D226E	probably damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Sema3g	G	A	14: 30,950,116 (GRCm39)	V766M	probably benign	Het
Skint6	T	A	4: 113,013,683 (GRCm39)	N356I	probably benign	Het
Slco2b1	A	T	7: 99,314,096 (GRCm39)	S496T	probably benign	Het
Trak1	T	C	9: 121,260,602 (GRCm39)	V11A	probably damaging	Het
Ubqlnl	C	T	7: 103,798,925 (GRCm39)	V191M	probably benign	Het
Umod	G	A	7: 119,065,287 (GRCm39)	P581S	probably damaging	Het
Zfat	A	G	15: 68,052,040 (GRCm39)	S585P	probably benign	Het
Zfp472	C	A	17: 33,197,134 (GRCm39)	T403N	probably benign	Het
Zfp936	A	G	7: 42,839,748 (GRCm39)	Q405R	possibly 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
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
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'- GCCCAAGCCAAGAGTTTAAAGTAG -3'
(R):5'- GGAGCCTATACCTGCATTGC -3'

Sequencing Primer
(F):5'- AGGCAGACCCTGGGGATAC -3'
(R):5'- ATTGCCACCAACCCTGCTG -3'

Posted On

2015-07-07