Mutagenetix > Incidental Mutation

Incidental Mutation 'R4938:Lrrc4c'

382821

Institutional Source

Beutler Lab

Gene Symbol

Lrrc4c

Ensembl Gene

ENSMUSG00000050587

Gene Name

leucine rich repeat containing 4C

Synonyms

6430556C10Rik, netrin g1 ligand, NGL-1

MMRRC Submission

042537-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.099) question?

Stock #

R4938 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

96148514-97462011 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 97459646 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 91 (I91F)

Ref Sequence

ENSEMBL: ENSMUSP00000125218 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000059049] [ENSMUST00000135431] [ENSMUST00000162807] [ENSMUST00000170144]

AlphaFold

Q8C031

Predicted Effect

probably damaging
Transcript: ENSMUST00000059049
AA Change: I91F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000131795
Gene: ENSMUSG00000050587
AA Change: I91F

Domain	Start	End	E-Value	Type
low complexity region	26	42	N/A	INTRINSIC
LRRNT	46	80	6.95e-4	SMART
LRR	79	98	1.97e2	SMART
LRR_TYP	99	122	7.37e-4	SMART
LRR	123	146	1.08e-1	SMART
LRR_TYP	147	170	1.38e-3	SMART
Blast:LRR	171	195	5e-8	BLAST
LRR	196	217	8.03e1	SMART
LRR_TYP	218	241	2.12e-4	SMART
LRR	242	265	6.97e1	SMART
LRR_TYP	266	289	2.53e-2	SMART
LRRCT	301	352	2.68e-2	SMART
IGc2	366	433	1.22e-7	SMART
transmembrane domain	526	548	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000135431
AA Change: I91F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000130984
Gene: ENSMUSG00000050587
AA Change: I91F

Domain	Start	End	E-Value	Type
low complexity region	26	42	N/A	INTRINSIC
LRRNT	46	80	6.95e-4	SMART
LRR	79	98	1.97e2	SMART
LRR_TYP	99	122	7.37e-4	SMART
LRR	123	146	1.08e-1	SMART
LRR_TYP	147	170	1.38e-3	SMART
Blast:LRR	171	195	5e-8	BLAST
LRR	196	217	8.03e1	SMART
LRR_TYP	218	241	2.12e-4	SMART
LRR	242	265	6.97e1	SMART
LRR_TYP	266	289	2.53e-2	SMART
LRRCT	301	352	2.68e-2	SMART
IGc2	366	433	1.22e-7	SMART
transmembrane domain	526	548	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000162807
AA Change: I91F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000125218
Gene: ENSMUSG00000050587
AA Change: I91F

Domain	Start	End	E-Value	Type
low complexity region	26	42	N/A	INTRINSIC
LRRNT	46	80	6.95e-4	SMART
LRR	79	98	1.97e2	SMART
LRR_TYP	99	122	7.37e-4	SMART
LRR	123	146	1.08e-1	SMART
LRR_TYP	147	170	1.38e-3	SMART
Blast:LRR	171	195	5e-8	BLAST
LRR	196	217	8.03e1	SMART
LRR_TYP	218	241	2.12e-4	SMART
LRR	242	265	6.97e1	SMART
LRR_TYP	266	289	2.53e-2	SMART
LRRCT	301	352	2.68e-2	SMART
IGc2	366	433	1.22e-7	SMART
transmembrane domain	526	548	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000170144

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199276

Meta Mutation Damage Score

0.2974

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.6%

Validation Efficiency

99% (74/75)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Homozygous mutant mice exhibited an increased mean serum IL-6 response to LPS challenge when compared with controls. No other notable phenotype was detected in a high-througput screen. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arl14ep	G	T	2: 106,799,663 (GRCm39)	H59Q	probably damaging	Het
Atp6v0a4	T	A	6: 38,055,749 (GRCm39)	I321F	possibly damaging	Het
Cdr2l	A	G	11: 115,284,651 (GRCm39)	D329G	possibly damaging	Het
Cep55	A	G	19: 38,058,364 (GRCm39)	E319G	probably damaging	Het
Cfhr2	C	T	1: 139,741,265 (GRCm39)	V237I	probably benign	Het
Clasrp	A	G	7: 19,318,703 (GRCm39)		probably null	Het
Col12a1	C	A	9: 79,607,632 (GRCm39)	E399*	probably null	Het
Cyp19a1	T	A	9: 54,080,647 (GRCm39)	I237F	probably benign	Het
Dnajc6	T	G	4: 101,494,010 (GRCm39)	N847K	probably damaging	Het
E330013P04Rik	C	G	19: 60,150,453 (GRCm39)		noncoding transcript	Het
Entpd2	A	G	2: 25,289,429 (GRCm39)	T304A	probably benign	Het
Etl4	A	G	2: 20,803,460 (GRCm39)	T779A	probably benign	Het
Fam107b	A	T	2: 3,773,907 (GRCm39)	I35L	probably benign	Het
Fgg	A	T	3: 82,920,175 (GRCm39)	Y318F	probably benign	Het
Fitm1	A	C	14: 55,814,076 (GRCm39)	T191P	probably damaging	Het
Fras1	A	G	5: 96,924,583 (GRCm39)	M3675V	probably damaging	Het
Fry	C	T	5: 150,401,454 (GRCm39)	R731W	probably damaging	Het
Galnt17	A	T	5: 131,335,237 (GRCm39)	S68T	probably benign	Het
Glp2r	G	T	11: 67,648,419 (GRCm39)	Y94*	probably null	Het
Grm1	C	T	10: 10,812,257 (GRCm39)	A256T	probably damaging	Het
Hoxd13	A	G	2: 74,499,027 (GRCm39)	Y125C	probably benign	Het
Hspa14	A	T	2: 3,492,646 (GRCm39)	I373K	probably benign	Het
Ifnlr1	A	G	4: 135,432,593 (GRCm39)	E343G	probably benign	Het
Ighv5-9	A	G	12: 113,625,582 (GRCm39)	S54P	probably benign	Het
Insyn2b	G	A	11: 34,352,231 (GRCm39)	G91E	probably damaging	Het
Irf2bpl	A	G	12: 86,928,892 (GRCm39)	S594P	possibly damaging	Het
Kcnq2	A	G	2: 180,728,766 (GRCm39)	S548P	probably damaging	Het
Lrp2	G	A	2: 69,302,712 (GRCm39)	R3006W	probably damaging	Het
Mdh1b	T	C	1: 63,750,663 (GRCm39)	D435G	probably benign	Het
Mettl3	A	T	14: 52,537,184 (GRCm39)	S182T	probably damaging	Het
Mllt6	A	G	11: 97,569,233 (GRCm39)	T862A	probably benign	Het
Mmp27	G	T	9: 7,578,983 (GRCm39)	R412I	probably damaging	Het
Mstn	A	G	1: 53,105,582 (GRCm39)	N308S	possibly damaging	Het
Ncapg	A	G	5: 45,828,551 (GRCm39)	T101A	probably benign	Het
Ngf	C	T	3: 102,427,790 (GRCm39)	R180W	probably damaging	Het
Notch1	G	A	2: 26,364,136 (GRCm39)	Q862*	probably null	Het
Nsrp1	T	C	11: 76,936,570 (GRCm39)	D542G	probably damaging	Het
Nup214	C	A	2: 31,873,171 (GRCm39)	T255K	probably benign	Het
Or5b21	T	A	19: 12,839,916 (GRCm39)	M259K	probably damaging	Het
Or8b43	T	A	9: 38,360,679 (GRCm39)	D170E	probably benign	Het
Papln	C	T	12: 83,829,677 (GRCm39)	P911S	probably benign	Het
Pdxdc1	A	G	16: 13,693,933 (GRCm39)	V163A	probably benign	Het
Plekhj1	A	T	10: 80,633,609 (GRCm39)	I76N	probably damaging	Het
Pnp2	A	G	14: 51,201,025 (GRCm39)		probably null	Het
Polr3gl	T	C	3: 96,487,208 (GRCm39)	E89G	probably benign	Het
Polrmt	A	G	10: 79,582,385 (GRCm39)	M1T	probably null	Het
Prss37	A	G	6: 40,491,917 (GRCm39)	I221T	possibly damaging	Het
Ptx4	C	T	17: 25,342,139 (GRCm39)	Q205*	probably null	Het
Qsox1	T	C	1: 155,655,414 (GRCm39)	E583G	probably benign	Het
Riok3	T	A	18: 12,288,300 (GRCm39)	N492K	probably benign	Het
Sec13	A	G	6: 113,712,153 (GRCm39)	W61R	probably damaging	Het
Slc20a2	T	C	8: 23,051,221 (GRCm39)	V418A	possibly damaging	Het
Smad9	G	A	3: 54,696,651 (GRCm39)	V239I	probably benign	Het
Stmn2	A	G	3: 8,610,792 (GRCm39)	E92G	probably damaging	Het
Taf1c	A	G	8: 120,325,537 (GRCm39)	V775A	probably benign	Het
Thsd7a	T	A	6: 12,330,991 (GRCm39)	I1384L	probably benign	Het
Tnxb	A	G	17: 34,932,606 (GRCm39)	Y2275C	probably damaging	Het
Trmo	G	T	4: 46,382,388 (GRCm39)	T243N	probably benign	Het
Tyrp1	C	T	4: 80,758,883 (GRCm39)	A252V	probably damaging	Het
Vasp	T	C	7: 18,991,642 (GRCm39)	*376W	probably null	Het
Vmn1r231	T	C	17: 21,110,613 (GRCm39)	I101V	possibly damaging	Het
Zfp532	T	C	18: 65,756,837 (GRCm39)	S257P	probably benign	Het
Zfp563	G	A	17: 33,324,683 (GRCm39)	C426Y	probably damaging	Het
Zfp647	TGCACG	TGCACGCACG	15: 76,795,244 (GRCm39)		probably null	Het
Zfp703	C	A	8: 27,469,801 (GRCm39)	H488Q	probably damaging	Het
Zfp964	A	G	8: 70,116,758 (GRCm39)	N452D	possibly damaging	Het
Zfyve28	A	C	5: 34,390,698 (GRCm39)	Y188D	probably damaging	Het

Other mutations in Lrrc4c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00482:Lrrc4c	APN	2	97,460,730 (GRCm39)	nonsense	probably null
IGL02095:Lrrc4c	APN	2	97,459,749 (GRCm39)	missense	probably benign	0.05
IGL02165:Lrrc4c	APN	2	97,459,378 (GRCm39)	start codon destroyed	probably null	0.33
IGL02176:Lrrc4c	APN	2	97,460,598 (GRCm39)	missense	probably damaging	0.96
IGL02674:Lrrc4c	APN	2	97,460,120 (GRCm39)	missense	probably damaging	0.99
IGL03082:Lrrc4c	APN	2	97,460,931 (GRCm39)	missense	probably benign	0.05
IGL03303:Lrrc4c	APN	2	97,459,937 (GRCm39)	missense	probably damaging	1.00
R0946:Lrrc4c	UTSW	2	97,459,809 (GRCm39)	missense	probably benign	0.00
R1037:Lrrc4c	UTSW	2	97,460,330 (GRCm39)	missense	probably benign
R1518:Lrrc4c	UTSW	2	97,460,921 (GRCm39)	missense	probably benign
R1559:Lrrc4c	UTSW	2	97,461,117 (GRCm39)	missense	probably benign	0.00
R2192:Lrrc4c	UTSW	2	97,459,657 (GRCm39)	missense	possibly damaging	0.50
R2213:Lrrc4c	UTSW	2	97,460,816 (GRCm39)	missense	probably benign	0.29
R2279:Lrrc4c	UTSW	2	97,460,850 (GRCm39)	missense	possibly damaging	0.86
R3552:Lrrc4c	UTSW	2	97,460,306 (GRCm39)	missense	probably damaging	1.00
R3840:Lrrc4c	UTSW	2	97,460,537 (GRCm39)	missense	probably damaging	0.98
R3841:Lrrc4c	UTSW	2	97,460,537 (GRCm39)	missense	probably damaging	0.98
R4606:Lrrc4c	UTSW	2	97,460,658 (GRCm39)	missense	probably benign	0.22
R4946:Lrrc4c	UTSW	2	97,460,834 (GRCm39)	missense	probably benign	0.00
R5323:Lrrc4c	UTSW	2	97,460,498 (GRCm39)	missense	probably damaging	1.00
R6014:Lrrc4c	UTSW	2	97,459,557 (GRCm39)	splice site	probably null
R6297:Lrrc4c	UTSW	2	97,459,964 (GRCm39)	missense	probably damaging	0.99
R6376:Lrrc4c	UTSW	2	97,459,391 (GRCm39)	missense	probably benign	0.03
R7032:Lrrc4c	UTSW	2	97,459,410 (GRCm39)	missense	probably benign
R7419:Lrrc4c	UTSW	2	97,460,106 (GRCm39)	missense	probably benign	0.07
R7699:Lrrc4c	UTSW	2	97,461,024 (GRCm39)	missense	possibly damaging	0.81
R7700:Lrrc4c	UTSW	2	97,461,024 (GRCm39)	missense	possibly damaging	0.81
R7723:Lrrc4c	UTSW	2	97,460,999 (GRCm39)	missense	possibly damaging	0.91
R7736:Lrrc4c	UTSW	2	97,460,705 (GRCm39)	missense	probably benign	0.02
R7843:Lrrc4c	UTSW	2	97,460,558 (GRCm39)	missense	probably benign	0.19
R7880:Lrrc4c	UTSW	2	97,461,143 (GRCm39)	missense	probably benign	0.08
R8008:Lrrc4c	UTSW	2	97,460,594 (GRCm39)	missense	possibly damaging	0.88
R8479:Lrrc4c	UTSW	2	97,459,977 (GRCm39)	missense	probably damaging	1.00
R8802:Lrrc4c	UTSW	2	97,460,603 (GRCm39)	missense	possibly damaging	0.83
R8821:Lrrc4c	UTSW	2	97,460,040 (GRCm39)	missense	possibly damaging	0.88
R8906:Lrrc4c	UTSW	2	97,460,393 (GRCm39)	missense	probably benign	0.00
R8933:Lrrc4c	UTSW	2	97,459,826 (GRCm39)	missense	probably benign	0.36
R8974:Lrrc4c	UTSW	2	97,459,992 (GRCm39)	missense	probably damaging	1.00
R9115:Lrrc4c	UTSW	2	97,459,686 (GRCm39)	missense	probably benign	0.00
R9266:Lrrc4c	UTSW	2	97,459,853 (GRCm39)	missense	probably benign	0.26
R9311:Lrrc4c	UTSW	2	97,461,080 (GRCm39)	missense	possibly damaging	0.90
Z1177:Lrrc4c	UTSW	2	97,460,828 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GGTGCTGTTGGCTCTTCAAC -3'
(R):5'- GATGCTTTCAATAGGGTTGTTCCTC -3'

Sequencing Primer
(F):5'- CTTCAACTTCTTGTGGTGGC -3'
(R):5'- AACCAGAGCTCCTTCAGTTTAG -3'

Posted On

2016-04-27