Mutagenetix > Incidental Mutation

Incidental Mutation 'R8482:Lrfn4'

657597

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

067926-MU

Accession Numbers

Essential gene?

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

Stock #

R8482 (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 4664333 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 67 (D67G)

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: D67G

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

SMART Domains

Protein: ENSMUSP00000050039
Gene: ENSMUSG00000045045
AA Change: D67G

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: D67G

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

SMART Domains

Protein: ENSMUSP00000109453
Gene: ENSMUSG00000045045
AA Change: D67G

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: 99.8%
20x: 99.4%

Validation Efficiency

100% (49/49)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acan	G	A	7: 78,746,492 (GRCm39)	V711I	probably benign	Het
Adprh	A	T	16: 38,267,871 (GRCm39)	M138K	probably damaging	Het
Ahctf1	A	G	1: 179,591,107 (GRCm39)		probably benign	Het
Atg9a	G	A	1: 75,162,870 (GRCm39)	T410M	probably damaging	Het
Atxn1	A	T	13: 45,721,426 (GRCm39)	S156R	possibly damaging	Het
Bptf	T	C	11: 106,934,524 (GRCm39)	T2850A	probably benign	Het
Cc2d2a	A	T	5: 43,852,581 (GRCm39)	Y386F	probably damaging	Het
Ccdc97	T	C	7: 25,414,427 (GRCm39)	D109G	probably damaging	Het
Chd5	C	T	4: 152,441,147 (GRCm39)	R196*	probably null	Het
Clec4a2	T	C	6: 123,100,630 (GRCm39)		probably null	Het
Col13a1	A	G	10: 61,720,477 (GRCm39)	I317T	probably damaging	Het
D630003M21Rik	G	T	2: 158,058,852 (GRCm39)	S349R	probably benign	Het
Eml5	C	A	12: 98,842,560 (GRCm39)	L179F	probably damaging	Het
Entrep1	T	A	19: 23,965,866 (GRCm39)	N211I	probably damaging	Het
Ets2	A	T	16: 95,516,019 (GRCm39)	M200L	probably benign	Het
Fat3	T	C	9: 16,158,263 (GRCm39)	T1116A	probably benign	Het
Fhit	A	G	14: 10,751,616 (GRCm38)	V24A	probably benign	Het
Gm6685	T	C	11: 28,289,195 (GRCm39)	N207S	probably benign	Het
Hdc	G	A	2: 126,436,125 (GRCm39)	T582M	probably benign	Het
Hmgxb4	G	A	8: 75,756,222 (GRCm39)	C575Y	probably damaging	Het
Kidins220	T	A	12: 25,090,527 (GRCm39)	S1164T	probably benign	Het
Ldb1	C	A	19: 46,024,709 (GRCm39)	D5Y	probably null	Het
Lpcat1	G	A	13: 73,659,044 (GRCm39)	R320H	probably benign	Het
Myo15b	C	T	11: 115,774,083 (GRCm39)	Q550*	probably null	Het
Myo18b	C	A	5: 113,019,489 (GRCm39)	E43*	probably null	Het
Neurl1a	T	C	19: 47,241,719 (GRCm39)	C271R	probably damaging	Het
Nfasc	T	C	1: 132,532,827 (GRCm39)	S690G	probably damaging	Het
Ngly1	T	C	14: 16,310,377 (GRCm38)	S501P	probably benign	Het
Nlrp1a	A	T	11: 70,999,901 (GRCm39)		probably null	Het
Npw	A	G	17: 24,876,396 (GRCm39)	W172R	probably benign	Het
Nudt8	T	C	19: 4,050,849 (GRCm39)		probably null	Het
Nyap2	A	T	1: 81,219,352 (GRCm39)	Y458F	probably damaging	Het
Or10ag56	G	A	2: 87,139,726 (GRCm39)	V198I	probably benign	Het
Osbpl5	T	A	7: 143,258,731 (GRCm39)	T280S	probably benign	Het
Pex1	A	T	5: 3,662,923 (GRCm39)	I505F	probably benign	Het
Pfkm	A	G	15: 98,029,864 (GRCm39)	E756G	probably benign	Het
Pkd2l2	A	G	18: 34,558,166 (GRCm39)	I282V	possibly damaging	Het
Pnpla8	T	C	12: 44,330,410 (GRCm39)	S321P	probably benign	Het
Prxl2a	C	T	14: 40,719,723 (GRCm39)	E164K	probably benign	Het
Qdpr	G	T	5: 45,596,688 (GRCm39)	Q159K	probably benign	Het
Rac2	T	C	15: 78,450,206 (GRCm39)	M45V	probably benign	Het
Rnaset2b	G	A	17: 7,263,908 (GRCm39)		probably null	Het
Rpl38	T	A	11: 114,563,114 (GRCm39)	*71R	probably null	Het
Sacs	G	T	14: 61,440,404 (GRCm39)	V817L	probably benign	Het
Selenot	T	C	3: 58,495,889 (GRCm39)	F133S	probably damaging	Het
Sgcg	G	A	14: 61,477,856 (GRCm39)	L78F	probably damaging	Het
Slc19a1	A	G	10: 76,885,497 (GRCm39)	R466G	probably benign	Het
Tpr	A	G	1: 150,309,451 (GRCm39)	T1736A	probably damaging	Het
Zfhx3	A	G	8: 109,674,511 (GRCm39)	I1854V	probably benign	Het
Zfp652	T	C	11: 95,643,719 (GRCm39)	S306P	probably damaging	Het
Zfp998	C	T	13: 66,579,797 (GRCm39)		probably benign	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
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
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'- TGCCACTGAGAATGAGATGCTG -3'
(R):5'- AACTGGTTCCTGGGACTGTG -3'

Sequencing Primer
(F):5'- ATGCTGGAGGTTGACAGGCC -3'
(R):5'- CTATTGCTGCTGCTGGCCAG -3'

Posted On

2021-01-18