Mutagenetix > Incidental Mutation

Incidental Mutation 'R0652:Lrrc28'

62294

Institutional Source

Beutler Lab

Gene Symbol

Lrrc28

Ensembl Gene

ENSMUSG00000030556

Gene Name

leucine rich repeat containing 28

Synonyms

2310058O11Rik, 2210012C09Rik, 1300004K21Rik

MMRRC Submission

038837-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.109) question?

Stock #

R0652 (G1)

Quality Score

107

Status

Not validated

Chromosome

Chromosomal Location

67163158-67295016 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 67267833 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 98 (N98S)

Ref Sequence

ENSEMBL: ENSMUSP00000052177 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032775] [ENSMUST00000053950] [ENSMUST00000187953] [ENSMUST00000189836] [ENSMUST00000190276] [ENSMUST00000191035]

AlphaFold

Q3TX51

Predicted Effect

probably benign
Transcript: ENSMUST00000032775
AA Change: N98S

PolyPhen 2 Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000032775
Gene: ENSMUSG00000030556
AA Change: N98S

Domain	Start	End	E-Value	Type
LRR	40	63	1.33e-1	SMART
LRR	64	86	3.24e0	SMART
LRR	87	109	1.06e1	SMART
LRR_TYP	110	132	7.78e-3	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000053950
AA Change: N98S

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

SMART Domains

Protein: ENSMUSP00000052177
Gene: ENSMUSG00000030556
AA Change: N98S

Domain	Start	End	E-Value	Type
LRR	40	63	1.33e-1	SMART
LRR	64	86	3.24e0	SMART
LRR	87	109	1.06e1	SMART
LRR_TYP	110	132	6.67e-2	SMART
LRR	133	156	6.4e0	SMART
LRR	179	202	1.64e-1	SMART
low complexity region	304	318	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000187953

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000188971

Predicted Effect

probably benign
Transcript: ENSMUST00000189836
AA Change: N107S

PolyPhen 2 Score 0.301 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000139606
Gene: ENSMUSG00000030556
AA Change: N107S

Domain	Start	End	E-Value	Type
Pfam:LRR_1	42	64	5.5e-2	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000190276
AA Change: N98S

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000140972
Gene: ENSMUSG00000030556
AA Change: N98S

Domain	Start	End	E-Value	Type
LRR	40	59	3.7e-3	SMART
LRR	64	83	1.2e0	SMART
LRR	87	109	4.4e-2	SMART
LRR_TYP	110	133	2.3e-6	SMART
LRR	133	153	1.1e0	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000190770

Predicted Effect

probably benign
Transcript: ENSMUST00000191035
AA Change: N98S

PolyPhen 2 Score 0.158 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000140382
Gene: ENSMUSG00000030556
AA Change: N98S

Domain	Start	End	E-Value	Type
LRR	40	63	1.33e-1	SMART
LRR	64	86	3.24e0	SMART
LRR	87	109	1.06e1	SMART
LRR	110	132	8.09e-1	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000191386

Meta Mutation Damage Score

0.4969

Coding Region Coverage

1x: 99.3%
3x: 98.5%
10x: 96.3%
20x: 90.1%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	T	C	11: 110,042,889 (GRCm39)	N387D	probably benign	Het
Adgrg5	T	A	8: 95,660,785 (GRCm39)		probably null	Het
Ahi1	C	A	10: 20,855,360 (GRCm39)	H556Q	probably damaging	Het
Amph	A	G	13: 19,270,791 (GRCm39)		probably null	Het
Apol7a	T	C	15: 77,274,055 (GRCm39)		probably benign	Het
Apoo-ps	A	T	13: 107,550,910 (GRCm39)		noncoding transcript	Het
Arpc1b	A	G	5: 145,063,670 (GRCm39)	D306G	probably damaging	Het
Astn2	T	C	4: 65,712,795 (GRCm39)	D615G	probably damaging	Het
Atm	A	G	9: 53,397,314 (GRCm39)	V1673A	probably damaging	Het
B3gnt3	A	T	8: 72,146,466 (GRCm39)	V21E	probably benign	Het
Bco1	A	G	8: 117,832,435 (GRCm39)	D77G	probably damaging	Het
Brinp2	A	T	1: 158,074,191 (GRCm39)	H643Q	probably damaging	Het
Bsn	A	G	9: 107,982,941 (GRCm39)	F3604S	unknown	Het
Cacna1c	A	G	6: 118,579,190 (GRCm39)	F1753L	probably damaging	Het
Cd74	T	C	18: 60,944,957 (GRCm39)	S201P	probably damaging	Het
Cep192	T	A	18: 67,940,336 (GRCm39)	L101Q	probably benign	Het
Cfap161	T	C	7: 83,442,484 (GRCm39)	I110V	probably null	Het
Cnksr3	T	C	10: 7,070,463 (GRCm39)	D257G	probably damaging	Het
Col14a1	A	C	15: 55,208,278 (GRCm39)	E121A	unknown	Het
Cpne3	T	C	4: 19,532,486 (GRCm39)	D309G	probably benign	Het
Ctnnd1	A	G	2: 84,433,240 (GRCm39)	I609T	probably benign	Het
Cyp2s1	A	G	7: 25,508,683 (GRCm39)	V253A	probably damaging	Het
Dock7	T	C	4: 98,943,586 (GRCm39)	D552G	possibly damaging	Het
Dpyd	A	G	3: 119,220,924 (GRCm39)	D965G	probably damaging	Het
Efcab2	T	A	1: 178,308,911 (GRCm39)	M138K	probably damaging	Het
Eml3	T	C	19: 8,910,649 (GRCm39)	S204P	probably damaging	Het
Fbxw16	T	A	9: 109,265,236 (GRCm39)	S432C	possibly damaging	Het
Fbxw20	T	G	9: 109,061,400 (GRCm39)	Q116H	probably damaging	Het
Fech	A	G	18: 64,591,240 (GRCm39)	S395P	probably damaging	Het
Fgf7	A	G	2: 125,877,875 (GRCm39)	K81E	probably benign	Het
Fras1	T	A	5: 96,929,199 (GRCm39)	Y3868N	possibly damaging	Het
Ganab	A	T	19: 8,892,766 (GRCm39)		probably null	Het
Gfra1	T	C	19: 58,288,986 (GRCm39)	N153S	possibly damaging	Het
Gja4	T	A	4: 127,205,920 (GRCm39)	Y281F	probably benign	Het
Gm5141	T	C	13: 62,921,946 (GRCm39)	T407A	probably damaging	Het
Gm5422	T	C	10: 31,125,277 (GRCm39)		noncoding transcript	Het
Greb1	T	C	12: 16,746,457 (GRCm39)	Y1271C	probably damaging	Het
Hp1bp3	C	A	4: 137,956,080 (GRCm39)	N50K	possibly damaging	Het
Hspg2	T	C	4: 137,242,033 (GRCm39)	F589S	probably damaging	Het
Ido1	A	G	8: 25,075,260 (GRCm39)	F183S	probably damaging	Het
Iqgap1	T	A	7: 80,386,143 (GRCm39)	K936I	probably damaging	Het
Kdm4a	T	C	4: 118,032,886 (GRCm39)	D60G	probably benign	Het
L3mbtl4	G	A	17: 69,081,286 (GRCm39)	C558Y	probably damaging	Het
Lypd11	T	A	7: 24,423,622 (GRCm39)	N14I	possibly damaging	Het
Map1a	A	G	2: 121,133,264 (GRCm39)	D1360G	probably benign	Het
Megf10	C	T	18: 57,410,796 (GRCm39)	P702S	probably benign	Het
Met	A	G	6: 17,491,709 (GRCm39)	E157G	probably benign	Het
Mff	A	G	1: 82,728,285 (GRCm39)	D187G	possibly damaging	Het
Mlph	A	T	1: 90,870,630 (GRCm39)	I514F	possibly damaging	Het
Mroh2a	C	T	1: 88,158,402 (GRCm39)	R150*	probably null	Het
Myo15b	T	C	11: 115,755,468 (GRCm39)	V976A	probably benign	Het
Myo9a	A	G	9: 59,779,209 (GRCm39)	D1655G	probably benign	Het
Ncoa6	C	T	2: 155,233,131 (GRCm39)	G2059D	probably benign	Het
Ndst4	A	T	3: 125,405,188 (GRCm39)	H481L	possibly damaging	Het
Nipbl	A	G	15: 8,332,964 (GRCm39)	S2220P	probably benign	Het
Nom1	C	A	5: 29,640,309 (GRCm39)	P212T	probably damaging	Het
Nsd1	A	G	13: 55,395,399 (GRCm39)	D1000G	possibly damaging	Het
Nudt9	T	C	5: 104,198,467 (GRCm39)	F44S	possibly damaging	Het
Numb	C	T	12: 83,842,566 (GRCm39)	V537I	probably damaging	Het
Or10j3b	T	A	1: 173,043,524 (GRCm39)	I102N	possibly damaging	Het
Or13a27	A	T	7: 139,925,545 (GRCm39)	M119K	probably damaging	Het
Or51q1c	A	G	7: 103,652,446 (GRCm39)		probably null	Het
Or5b109	A	T	19: 13,211,899 (GRCm39)	Y95F	possibly damaging	Het
Or5h17	A	G	16: 58,820,063 (GRCm39)	N5S	probably damaging	Het
Or6c211	T	A	10: 129,506,248 (GRCm39)	T47S	probably benign	Het
Osgin1	A	T	8: 120,172,211 (GRCm39)	Y335F	probably damaging	Het
Pcdh10	T	A	3: 45,334,199 (GRCm39)	V171E	probably damaging	Het
Pira13	T	A	7: 3,825,762 (GRCm39)	Y369F	probably benign	Het
Plxna4	T	C	6: 32,162,436 (GRCm39)	N1359S	probably damaging	Het
Ppp1r16a	C	T	15: 76,574,999 (GRCm39)		probably benign	Het
Prr5l	T	C	2: 101,602,635 (GRCm39)	T2A	possibly damaging	Het
Rbp3	T	A	14: 33,680,605 (GRCm39)	I1069N	possibly damaging	Het
Rnf144b	A	G	13: 47,373,983 (GRCm39)	Y60C	probably damaging	Het
Sbno2	A	T	10: 79,903,128 (GRCm39)	V396E	probably damaging	Het
Sdk1	A	G	5: 141,940,713 (GRCm39)	T494A	probably benign	Het
Serac1	G	T	17: 6,102,031 (GRCm39)	D384E	probably damaging	Het
Sgk1	A	G	10: 21,758,556 (GRCm39)	N7D	probably damaging	Het
Sigirr	A	T	7: 140,672,980 (GRCm39)	V69D	possibly damaging	Het
Slc17a3	C	T	13: 24,039,841 (GRCm39)	S293F	probably damaging	Het
St6gal2	T	C	17: 55,805,290 (GRCm39)	Y396H	probably benign	Het
Ttn	A	T	2: 76,598,956 (GRCm39)	F19319Y	probably damaging	Het
Ubr4	T	A	4: 139,128,637 (GRCm39)	I599N	probably damaging	Het
Vmn1r213	A	G	13: 23,195,564 (GRCm39)		probably benign	Het
Vmn2r96	T	A	17: 18,817,830 (GRCm39)	M469K	probably benign	Het
Wasf1	T	A	10: 40,807,902 (GRCm39)		probably null	Het
Wdr20rt	T	C	12: 65,272,689 (GRCm39)	S51P	probably damaging	Het

Other mutations in Lrrc28

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01548:Lrrc28	APN	7	67,278,042 (GRCm39)	critical splice donor site	probably null
IGL01583:Lrrc28	APN	7	67,195,223 (GRCm39)	splice site	probably null
IGL02033:Lrrc28	APN	7	67,209,605 (GRCm39)	critical splice donor site	probably null
IGL02483:Lrrc28	APN	7	67,267,731 (GRCm39)	splice site	probably benign
IGL02750:Lrrc28	APN	7	67,181,431 (GRCm39)	missense	probably damaging	0.96
BB002:Lrrc28	UTSW	7	67,268,857 (GRCm39)	missense	probably damaging	1.00
BB012:Lrrc28	UTSW	7	67,268,857 (GRCm39)	missense	probably damaging	1.00
R0549:Lrrc28	UTSW	7	67,278,090 (GRCm39)	splice site	probably benign
R0563:Lrrc28	UTSW	7	67,195,135 (GRCm39)	missense	probably damaging	1.00
R0650:Lrrc28	UTSW	7	67,267,833 (GRCm39)	missense	probably damaging	1.00
R1557:Lrrc28	UTSW	7	67,209,677 (GRCm39)	missense	probably damaging	1.00
R1820:Lrrc28	UTSW	7	67,290,859 (GRCm39)	missense	probably damaging	0.98
R2149:Lrrc28	UTSW	7	67,181,430 (GRCm39)	missense	probably damaging	0.96
R2185:Lrrc28	UTSW	7	67,195,201 (GRCm39)	missense	possibly damaging	0.70
R4479:Lrrc28	UTSW	7	67,181,362 (GRCm39)	critical splice donor site	probably null
R5205:Lrrc28	UTSW	7	67,181,516 (GRCm39)	missense	probably benign	0.00
R7008:Lrrc28	UTSW	7	67,245,459 (GRCm39)	intron	probably benign
R7925:Lrrc28	UTSW	7	67,268,857 (GRCm39)	missense	probably damaging	1.00
R8323:Lrrc28	UTSW	7	67,245,455 (GRCm39)	missense	unknown
R8360:Lrrc28	UTSW	7	67,290,909 (GRCm39)	missense	probably benign	0.01
R8898:Lrrc28	UTSW	7	67,278,042 (GRCm39)	critical splice donor site	probably null
R8919:Lrrc28	UTSW	7	67,268,833 (GRCm39)	missense	possibly damaging	0.88
R9412:Lrrc28	UTSW	7	67,181,512 (GRCm39)	missense	probably damaging	1.00
Z1088:Lrrc28	UTSW	7	67,179,379 (GRCm39)	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- CCTTGCCCAGCAGTGAGAAGAGTG -3'
(R):5'- ATCTGAGGTGGGCTCCTGTGTCTCC -3'

Sequencing Primer
(F):5'- ATTTACACCGGGTTCTCAGAACG -3'
(R):5'- TTTATCTCAAGAGATGCTTTCCAC -3'

Posted On

2013-07-30