Mutagenetix > Incidental Mutation

Incidental Mutation 'R7661:Lrrc4'

591561

Institutional Source

Beutler Lab

Gene Symbol

Lrrc4

Ensembl Gene

ENSMUSG00000049939

Gene Name

leucine rich repeat containing 4

Synonyms

Nag14, NGL-2, NGL2

MMRRC Submission

045736-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.208) question?

Stock #

R7661 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

28828125-28831746 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 28829762 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 618 (T618A)

Ref Sequence

ENSEMBL: ENSMUSP00000062158 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001460] [ENSMUST00000062304] [ENSMUST00000164915] [ENSMUST00000167201] [ENSMUST00000171353]

AlphaFold

Q99PH1

Predicted Effect

probably benign
Transcript: ENSMUST00000001460

SMART Domains

Protein: ENSMUSP00000001460
Gene: ENSMUSG00000001424

Domain	Start	End	E-Value	Type
low complexity region	2	15	N/A	INTRINSIC
SNc	18	166	7.12e-54	SMART
SNc	193	328	8.37e-51	SMART
SNc	341	496	4.11e-59	SMART
SNc	525	660	3.82e-45	SMART
TUDOR	728	785	4.8e-19	SMART
Pfam:SNase	835	895	1.3e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000062304
AA Change: T618A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000062158
Gene: ENSMUSG00000049939
AA Change: T618A

Domain	Start	End	E-Value	Type
low complexity region	32	40	N/A	INTRINSIC
LRRNT	44	78	4.05e-5	SMART
LRR	72	96	1.19e2	SMART
LRR_TYP	97	120	2.24e-3	SMART
LRR	121	144	6.13e-1	SMART
LRR_TYP	145	168	5.99e-4	SMART
LRR	216	239	1.25e-1	SMART
LRR	240	263	4.71e1	SMART
LRR_TYP	264	287	2.79e-4	SMART
LRRCT	299	350	8.06e-6	SMART
IGc2	364	430	5.24e-7	SMART
low complexity region	452	462	N/A	INTRINSIC
transmembrane domain	527	549	N/A	INTRINSIC
low complexity region	575	586	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000164915

SMART Domains

Protein: ENSMUSP00000127317
Gene: ENSMUSG00000001424

Domain	Start	End	E-Value	Type
low complexity region	2	15	N/A	INTRINSIC
SNc	18	142	1.56e-18	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000167201

SMART Domains

Protein: ENSMUSP00000128737
Gene: ENSMUSG00000001424

Domain	Start	End	E-Value	Type
low complexity region	2	15	N/A	INTRINSIC
SNc	18	166	7.12e-54	SMART
SNc	193	328	8.37e-51	SMART
SNc	341	496	4.11e-59	SMART
SCOP:d1sty__	526	592	1e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000171353

SMART Domains

Protein: ENSMUSP00000129497
Gene: ENSMUSG00000049939

Domain	Start	End	E-Value	Type
low complexity region	29	39	N/A	INTRINSIC
transmembrane domain	104	126	N/A	INTRINSIC
low complexity region	152	163	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

96% (50/52)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is significantly downregulated in primary brain tumors. The exact function of the protein encoded by this gene is unknown. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit hyperactivity, an absence of startle reflex, and abnormal ABR amplitude. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110018I06Rik	A	T	12: 107,455,215 (GRCm39)	K100N	unknown	Het
Abi3bp	T	A	16: 56,453,263 (GRCm39)		probably null	Het
Akr1c20	T	C	13: 4,558,218 (GRCm39)	D210G	probably benign	Het
Arid5b	C	T	10: 67,934,417 (GRCm39)	G495E	probably benign	Het
Ascc1	A	C	10: 59,885,629 (GRCm39)	N227H	probably damaging	Het
Atp5f1a	G	T	18: 77,861,802 (GRCm39)	A18S	possibly damaging	Het
Bcl2l13	A	G	6: 120,842,558 (GRCm39)	T84A	possibly damaging	Het
Blmh	T	A	11: 76,877,341 (GRCm39)	V419D	probably damaging	Het
Cacna1d	G	A	14: 29,769,177 (GRCm39)	P1918S	probably benign	Het
Calr4	T	C	4: 109,110,951 (GRCm39)	V339A	probably benign	Het
Capza3	C	A	6: 139,987,498 (GRCm39)	D32E	probably benign	Het
Cilk1	G	C	9: 78,074,902 (GRCm39)	V586L	probably benign	Het
Cldn20	T	A	17: 3,583,133 (GRCm39)	M102K	possibly damaging	Het
Dennd1a	T	C	2: 37,734,841 (GRCm39)	Q479R	probably benign	Het
Dpp10	A	T	1: 123,312,681 (GRCm39)	I432N	probably damaging	Het
Dst	T	A	1: 34,295,434 (GRCm39)		probably null	Het
Efcab3	T	A	11: 104,617,503 (GRCm39)	D741E	probably benign	Het
Fam135a	C	T	1: 24,111,843 (GRCm39)		probably null	Het
Fam47e	C	T	5: 92,735,384 (GRCm39)	L206F	probably damaging	Het
Focad	G	A	4: 88,221,772 (GRCm39)	R714H	unknown	Het
Hace1	T	G	10: 45,481,649 (GRCm39)	V124G	probably damaging	Het
Ifit1bl2	T	A	19: 34,596,428 (GRCm39)	Y396F	probably damaging	Het
Il22ra2	A	G	10: 19,497,826 (GRCm39)	I13M	probably benign	Het
Kif21a	A	G	15: 90,865,122 (GRCm39)	F517L	possibly damaging	Het
Mdn1	A	G	4: 32,691,229 (GRCm39)	T952A	probably benign	Het
Mindy3	A	T	2: 12,402,328 (GRCm39)	I208K	probably damaging	Het
Mug1	C	A	6: 121,838,179 (GRCm39)	H470N	possibly damaging	Het
Mycbp2	A	G	14: 103,450,059 (GRCm39)	I1744T	probably damaging	Het
Nanog	A	T	6: 122,690,431 (GRCm39)	R279W	probably damaging	Het
Ncoa2	T	A	1: 13,244,761 (GRCm39)	T646S	probably damaging	Het
Ndufa5	A	G	6: 24,518,724 (GRCm39)	*117R	probably null	Het
Nudt18	A	T	14: 70,817,276 (GRCm39)	E293D	probably benign	Het
Or1e22	A	G	11: 73,377,426 (GRCm39)	S75P	probably damaging	Het
Or51aa2	A	T	7: 103,187,826 (GRCm39)	V205E	probably damaging	Het
Paip1	C	T	13: 119,587,306 (GRCm39)	T390I	possibly damaging	Het
Pigg	G	A	5: 108,486,485 (GRCm39)	V713I	probably benign	Het
Pih1d2	T	C	9: 50,529,558 (GRCm39)		probably null	Het
Ppp2r3d	A	G	9: 124,442,696 (GRCm38)	F17L		Het
Ptprk	T	C	10: 28,342,036 (GRCm39)	I481T	probably benign	Het
Pygo2	T	C	3: 89,338,038 (GRCm39)		probably null	Het
Raet1d	T	C	10: 22,248,156 (GRCm39)	S225P	possibly damaging	Het
Rnf24	T	C	2: 131,164,135 (GRCm39)		probably benign	Het
Ror1	A	G	4: 100,298,687 (GRCm39)	S687G	probably damaging	Het
Rsph9	A	G	17: 46,446,013 (GRCm39)	S186P	probably damaging	Het
Sash1	C	T	10: 8,605,155 (GRCm39)	M1078I	probably benign	Het
Scd4	C	A	19: 44,327,510 (GRCm39)	D195E	probably benign	Het
Spopfm3	C	T	3: 94,105,709 (GRCm39)	T9I	probably damaging	Het
Syn3	A	G	10: 85,904,940 (GRCm39)	C348R	probably damaging	Het
Uspl1	T	C	5: 149,151,827 (GRCm39)	F1009S	probably benign	Het
Vmn1r2	T	A	4: 3,172,149 (GRCm39)	F23I	probably benign	Het
Vmn1r257	A	G	7: 22,391,229 (GRCm39)	S172P	probably benign	Het
Vmn2r-ps158	T	A	7: 42,672,582 (GRCm39)	N72K	probably benign	Het
Zfp747l1	A	T	7: 126,984,135 (GRCm39)	C322*	probably null	Het
Zfp839	C	T	12: 110,835,226 (GRCm39)	T827I	probably benign	Het

Other mutations in Lrrc4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02230:Lrrc4	APN	6	28,830,879 (GRCm39)	missense	probably damaging	0.99
IGL03223:Lrrc4	APN	6	28,831,469 (GRCm39)	missense	probably damaging	1.00
IGL03410:Lrrc4	APN	6	28,830,515 (GRCm39)	missense	probably damaging	1.00
R0233:Lrrc4	UTSW	6	28,829,734 (GRCm39)	missense	probably benign	0.05
R0233:Lrrc4	UTSW	6	28,829,734 (GRCm39)	missense	probably benign	0.05
R0456:Lrrc4	UTSW	6	28,831,103 (GRCm39)	missense	probably damaging	1.00
R1162:Lrrc4	UTSW	6	28,831,083 (GRCm39)	missense	probably damaging	1.00
R2001:Lrrc4	UTSW	6	28,830,904 (GRCm39)	missense	probably damaging	1.00
R2089:Lrrc4	UTSW	6	28,830,586 (GRCm39)	missense	probably benign	0.45
R2091:Lrrc4	UTSW	6	28,830,586 (GRCm39)	missense	probably benign	0.45
R2091:Lrrc4	UTSW	6	28,830,586 (GRCm39)	missense	probably benign	0.45
R2353:Lrrc4	UTSW	6	28,831,451 (GRCm39)	missense	probably benign	0.00
R5079:Lrrc4	UTSW	6	28,830,769 (GRCm39)	missense	possibly damaging	0.69
R5197:Lrrc4	UTSW	6	28,830,142 (GRCm39)	missense	probably damaging	1.00
R6701:Lrrc4	UTSW	6	28,830,905 (GRCm39)	missense	possibly damaging	0.95
R6755:Lrrc4	UTSW	6	28,831,292 (GRCm39)	missense	probably damaging	1.00
R7660:Lrrc4	UTSW	6	28,829,816 (GRCm39)	missense	probably benign	0.00
R8113:Lrrc4	UTSW	6	28,829,902 (GRCm39)	missense	probably damaging	0.97
R8272:Lrrc4	UTSW	6	28,662,192 (GRCm39)	missense	unknown
R9074:Lrrc4	UTSW	6	28,831,595 (GRCm39)	missense	probably damaging	0.99
R9094:Lrrc4	UTSW	6	28,830,206 (GRCm39)	missense	possibly damaging	0.92
R9197:Lrrc4	UTSW	6	28,831,318 (GRCm39)	missense	probably benign	0.01
R9447:Lrrc4	UTSW	6	28,830,650 (GRCm39)	missense	probably benign	0.08
R9803:Lrrc4	UTSW	6	28,662,199 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CTCCCCACTCTGTACAAAAGTTG -3'
(R):5'- CTGCTGCCATGTTGATTGTC -3'

Sequencing Primer
(F):5'- GAGTTTCCTGTACCTTGTCC -3'
(R):5'- GTCTTCTATAAACTTCGCAAGCGG -3'

Posted On

2019-11-12