Mutagenetix > Incidental Mutation

Incidental Mutation 'R8821:Lrrc4c'

673024

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

068654-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.081) question?

Stock #

R8821 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

96148514-97462011 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 97460040 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 222 (D222V)

Ref Sequence

ENSEMBL: ENSMUSP00000131795 (fasta)

Gene Model

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

AlphaFold

Q8C031

Predicted Effect

possibly damaging
Transcript: ENSMUST00000059049
AA Change: D222V

PolyPhen 2 Score 0.882 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000131795
Gene: ENSMUSG00000050587
AA Change: D222V

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

possibly damaging
Transcript: ENSMUST00000135431
AA Change: D222V

PolyPhen 2 Score 0.882 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000130984
Gene: ENSMUSG00000050587
AA Change: D222V

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

possibly damaging
Transcript: ENSMUST00000162807
AA Change: D222V

PolyPhen 2 Score 0.882 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000125218
Gene: ENSMUSG00000050587
AA Change: D222V

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

Meta Mutation Damage Score

0.1376

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (74/74)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A230072I06Rik	A	T	8: 12,329,688 (GRCm39)	I48L	unknown	Het
Abca8a	A	T	11: 109,949,362 (GRCm39)	I927K	probably damaging	Het
Abcc3	A	C	11: 94,241,787 (GRCm39)	C1415G	probably damaging	Het
Abcf3	C	T	16: 20,369,214 (GRCm39)	R205C	probably damaging	Het
Aldh3a1	A	G	11: 61,107,142 (GRCm39)	Y282C	probably damaging	Het
Alyref	CCCGCGCGGCGGCCTGCACTGCGCCGCCGCGGCCGCCCTGGGAGCCGGCCCTGCCGCG	CCCGCG	11: 120,489,023 (GRCm39)		probably null	Het
Arfgef3	A	G	10: 18,528,491 (GRCm39)	S299P	possibly damaging	Het
Asic2	A	T	11: 81,858,726 (GRCm39)	N95K	probably damaging	Het
Atp2c2	A	G	8: 120,476,033 (GRCm39)		probably null	Het
Btbd18	A	G	2: 84,497,601 (GRCm39)	D413G	probably damaging	Het
C8b	A	G	4: 104,647,874 (GRCm39)	Y355C	probably damaging	Het
Carm1	A	G	9: 21,491,663 (GRCm39)	E244G	probably damaging	Het
Castor2	T	A	5: 134,164,092 (GRCm39)	V96E	possibly damaging	Het
Catsperg1	A	T	7: 28,904,361 (GRCm39)		probably benign	Het
Cish	T	A	9: 107,177,671 (GRCm39)	F116I	probably damaging	Het
Ckmt1	G	A	2: 121,191,302 (GRCm39)		probably benign	Het
Clasrp	C	T	7: 19,320,362 (GRCm39)	R432H	unknown	Het
Clstn1	G	A	4: 149,730,780 (GRCm39)	R837Q	probably benign	Het
Col27a1	A	G	4: 63,143,148 (GRCm39)	T279A	probably benign	Het
Cox10	A	G	11: 63,855,306 (GRCm39)	F325S	probably damaging	Het
Cpne5	T	C	17: 29,430,668 (GRCm39)	I81V	probably benign	Het
Ctps1	A	T	4: 120,424,507 (GRCm39)	S36T	possibly damaging	Het
Dchs2	T	C	3: 83,192,670 (GRCm39)	L1705P	probably benign	Het
Dcstamp	A	G	15: 39,618,185 (GRCm39)	H198R	probably benign	Het
Dhx58	T	A	11: 100,594,806 (GRCm39)	K30M	probably damaging	Het
Dnah1	C	T	14: 31,018,455 (GRCm39)	A1392T	probably benign	Het
Dnah14	C	A	1: 181,619,569 (GRCm39)	Y3964*	probably null	Het
Dnah8	T	C	17: 31,013,712 (GRCm39)	S3818P	probably damaging	Het
Dnmt3b	T	A	2: 153,518,734 (GRCm39)	N632K	probably benign	Het
Drc7	G	A	8: 95,788,845 (GRCm39)	R301Q	probably damaging	Het
Dsg1a	T	C	18: 20,453,365 (GRCm39)	V21A	probably damaging	Het
Dtd1	T	C	2: 144,459,261 (GRCm39)	L95P	probably benign	Het
Efhb	A	T	17: 53,707,772 (GRCm39)		probably benign	Het
Fam186b	T	A	15: 99,178,733 (GRCm39)	M198L	possibly damaging	Het
Fam193a	A	G	5: 34,616,374 (GRCm39)	T850A	probably benign	Het
Fan1	G	A	7: 64,004,249 (GRCm39)	P739L	probably damaging	Het
Flii	A	T	11: 60,616,074 (GRCm39)	N28K	probably benign	Het
Fmo3	T	C	1: 162,796,407 (GRCm39)	Y55C	probably damaging	Het
Gfi1	G	A	5: 107,868,138 (GRCm39)	R377C	probably damaging	Het
Gm9195	C	T	14: 72,717,536 (GRCm39)	E266K	possibly damaging	Het
Hdac1-ps	T	A	17: 78,799,969 (GRCm39)	L320Q	probably damaging	Het
Helz	A	T	11: 107,525,919 (GRCm39)	M825L	probably damaging	Het
Hsd3b9	A	T	3: 98,354,047 (GRCm39)	W151R	probably benign	Het
Ift80	G	A	3: 68,869,583 (GRCm39)	A236V	probably damaging	Het
Il1rn	A	T	2: 24,239,505 (GRCm39)	T134S	possibly damaging	Het
Imp4	T	C	1: 34,483,445 (GRCm39)	M257T	probably benign	Het
Impdh2	T	C	9: 108,441,957 (GRCm39)	L377S	probably damaging	Het
Kcnrg	T	C	14: 61,844,981 (GRCm39)	V7A	possibly damaging	Het
Kdm1b	C	A	13: 47,217,617 (GRCm39)	L359I	possibly damaging	Het
Lima1	T	A	15: 99,704,306 (GRCm39)	T288S	probably benign	Het
Lrrc37	A	T	11: 103,510,470 (GRCm39)	D499E	unknown	Het
Mybpc3	T	A	2: 90,948,524 (GRCm39)	V4E	probably null	Het
Ncor1	A	T	11: 62,260,234 (GRCm39)	D505E	probably benign	Het
Nell1	A	G	7: 50,476,097 (GRCm39)	S579G	probably damaging	Het
Npc1	T	A	18: 12,333,877 (GRCm39)	M735L	probably benign	Het
Or1j13	G	A	2: 36,369,794 (GRCm39)	T116I	possibly damaging	Het
Or2at4	A	G	7: 99,384,893 (GRCm39)	H181R	possibly damaging	Het
Or4a73	A	G	2: 89,420,880 (GRCm39)	I193T	probably damaging	Het
Pcdhb12	A	G	18: 37,570,386 (GRCm39)	M511V	probably benign	Het
Peli2	G	A	14: 48,490,130 (GRCm39)	E201K	possibly damaging	Het
Phf3	T	A	1: 30,860,347 (GRCm39)	K828*	probably null	Het
Pih1d1	A	G	7: 44,806,196 (GRCm39)	D44G	possibly damaging	Het
Prag1	A	T	8: 36,613,891 (GRCm39)	T1148S	probably benign	Het
Ptpn18	A	T	1: 34,511,271 (GRCm39)	R338W	probably null	Het
Slc7a6os	A	T	8: 106,937,189 (GRCm39)	D90E	probably benign	Het
Sp7	T	A	15: 102,267,227 (GRCm39)	H211L	possibly damaging	Het
Ssh3	A	G	19: 4,319,053 (GRCm39)	V19A	possibly damaging	Het
Tcp11l2	A	G	10: 84,449,522 (GRCm39)	I496V	probably damaging	Het
Tenm3	C	T	8: 48,729,417 (GRCm39)	A1530T		Het
Tmem232	A	G	17: 65,743,367 (GRCm39)	L308P	probably damaging	Het
Tulp4	A	G	17: 6,189,409 (GRCm39)	N77S	probably damaging	Het
Unc13d	AATGCCTCCCATGCC	AATGCCTCCCATGCCTCCCATGCC	11: 115,958,998 (GRCm39)		probably benign	Het
Usp48	A	T	4: 137,341,080 (GRCm39)	D360V	probably damaging	Het
Vmn2r84	G	A	10: 130,226,968 (GRCm39)	A290V	probably benign	Het
Zfp1007	A	T	5: 109,824,174 (GRCm39)	S425R	probably benign	Het
Zfp512b	T	C	2: 181,228,525 (GRCm39)	N738S	probably benign	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
R4938:Lrrc4c	UTSW	2	97,459,646 (GRCm39)	missense	probably damaging	1.00
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
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'- AGGAGCTCTGGTTGAGGAAC -3'
(R):5'- CTCTCTAGATGATGCAAGGGTG -3'

Sequencing Primer
(F):5'- TTGAGGAACAACCCTATTGAAAGC -3'
(R):5'- GGTCATGAGGCAATAATGTTAGATTG -3'

Posted On

2021-04-30