Mutagenetix > Incidental Mutation

Incidental Mutation 'R6115:Lrfn4'

485102

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

044264-MU

Accession Numbers

Essential gene?

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

Stock #

R6115 (G1)

Quality Score

97.0078

Status

Validated

Chromosome

Chromosomal Location

4661813-4665695 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 4663937 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 199 (D199G)

Ref Sequence

ENSEMBL: ENSMUSP00000109453 (fasta)

Gene Model

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

AlphaFold

Q80XU8

Predicted Effect

probably damaging
Transcript: ENSMUST00000053597
AA Change: D199G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000050039
Gene: ENSMUSG00000045045
AA Change: D199G

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: D199G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000109453
Gene: ENSMUSG00000045045
AA Change: D199G

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

0.3775

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.9%

Validation Efficiency

98% (51/52)

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	C	G	5: 64,055,317 (GRCm39)	Q18E	probably damaging	Het
Acsf3	T	A	8: 123,517,411 (GRCm39)	H402Q	probably damaging	Het
Adam34	T	G	8: 44,105,098 (GRCm39)	Q182H	probably benign	Het
Alx1	G	A	10: 102,864,304 (GRCm39)	P55L	possibly damaging	Het
Arhgef38	A	T	3: 132,838,374 (GRCm39)		probably null	Het
Ccdc102a	T	C	8: 95,629,999 (GRCm39)	N514S	probably benign	Het
Corin	T	A	5: 72,518,072 (GRCm39)	T317S	probably damaging	Het
Ctnna2	A	G	6: 77,613,822 (GRCm39)	V256A	probably benign	Het
Dhx29	A	T	13: 113,089,335 (GRCm39)		probably null	Het
Dnah2	C	A	11: 69,337,475 (GRCm39)	D3209Y	probably damaging	Het
Dnhd1	A	G	7: 105,363,194 (GRCm39)	T3919A	probably benign	Het
F7	T	A	8: 13,083,958 (GRCm39)	N214K	probably benign	Het
Fam3b	T	G	16: 97,276,568 (GRCm39)	Q177H	possibly damaging	Het
Fign	T	C	2: 63,809,654 (GRCm39)	I539V	probably benign	Het
Hc	T	G	2: 34,903,050 (GRCm39)	D1067A	probably damaging	Het
Herc6	A	G	6: 57,560,191 (GRCm39)	D77G	probably benign	Het
Hmg20a	A	T	9: 56,397,116 (GRCm39)	E305D	possibly damaging	Het
Il16	G	A	7: 83,301,775 (GRCm39)	Q116*	probably null	Het
Kif13a	T	A	13: 46,954,789 (GRCm39)	I648F	probably damaging	Het
Lactb	G	T	9: 66,874,969 (GRCm39)	N374K	possibly damaging	Het
Lmx1b	T	C	2: 33,459,118 (GRCm39)	D145G	probably damaging	Het
Lrrc49	A	T	9: 60,522,444 (GRCm39)	V307E	possibly damaging	Het
Magi1	A	C	6: 93,685,051 (GRCm39)	S776A	possibly damaging	Het
Mthfsl	T	A	9: 88,570,807 (GRCm39)	*147L	probably null	Het
Nsmce4a	G	T	7: 130,148,722 (GRCm39)	Q95K	probably benign	Het
Or1j15	A	T	2: 36,458,963 (GRCm39)	M118L	probably damaging	Het
Or4k37	A	G	2: 111,159,558 (GRCm39)	T265A	probably benign	Het
Or4k49	A	T	2: 111,494,987 (GRCm39)	K139*	probably null	Het
Or5b24	T	C	19: 12,912,948 (GRCm39)	V282A	possibly damaging	Het
Pcdha7	A	G	18: 37,107,788 (GRCm39)	E271G	probably damaging	Het
Pcdhga8	T	A	18: 37,860,596 (GRCm39)	F551I	possibly damaging	Het
Prpf31	T	C	7: 3,642,705 (GRCm39)		probably null	Het
Qrfpr	C	T	3: 36,236,742 (GRCm39)	V220I	possibly damaging	Het
Rnf170	T	C	8: 26,615,994 (GRCm39)	F95S	possibly damaging	Het
Scn9a	T	A	2: 66,393,973 (GRCm39)	Y200F	possibly damaging	Het
Sfpq	A	T	4: 126,915,141 (GRCm39)		probably null	Het
Slc9c1	A	T	16: 45,376,132 (GRCm39)	Y406F	probably damaging	Het
Stk32c	G	T	7: 138,700,628 (GRCm39)	Y200*	probably null	Het
Svil	A	G	18: 5,108,675 (GRCm39)	R1938G	probably damaging	Het
Sycp2	G	C	2: 177,990,038 (GRCm39)	R1403G	probably benign	Het
Tm9sf4	T	C	2: 153,024,409 (GRCm39)		probably null	Het
Tmc3	A	T	7: 83,264,170 (GRCm39)	M633L	possibly damaging	Het
Tmem163	T	C	1: 127,605,185 (GRCm39)	D61G	possibly damaging	Het
Unc5b	C	A	10: 60,613,325 (GRCm39)	A304S	probably benign	Het
Vmn2r106	G	A	17: 20,488,638 (GRCm39)	P587L	probably benign	Het
Vmn2r18	A	T	5: 151,508,462 (GRCm39)	S221T	possibly damaging	Het
Vmn2r85	T	G	10: 130,258,672 (GRCm39)	Y461S	probably damaging	Het
Yod1	T	C	1: 130,646,800 (GRCm39)	F226L	possibly damaging	Het
Zbtb4	T	C	11: 69,667,148 (GRCm39)	I151T	probably damaging	Het
Zfp110	A	T	7: 12,583,701 (GRCm39)	Q783L	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
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'- AGGCTCACAGGAGAACTCTC -3'
(R):5'- TCAGTGGCAATCAACTGGG -3'

Sequencing Primer
(F):5'- GAGAACTCTCCCTCAGGCACTG -3'
(R):5'- AATCAACTGGGCCGCATCG -3'

Posted On

2017-08-16