Mutagenetix > Incidental Mutation

Incidental Mutation 'R1820:Lrrc28'

204785

Institutional Source

Beutler Lab

Gene Symbol

Lrrc28

Ensembl Gene

ENSMUSG00000030556

Gene Name

leucine rich repeat containing 28

Synonyms

2310058O11Rik, 2210012C09Rik, 1300004K21Rik

MMRRC Submission

039848-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.089) question?

Stock #

R1820 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

67163158-67295016 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 67290859 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Lysine at position 54 (T54K)

Ref Sequence

ENSEMBL: ENSMUSP00000052177 (fasta)

Gene Model

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

AlphaFold

Q3TX51

Predicted Effect

possibly damaging
Transcript: ENSMUST00000032775
AA Change: T54K

PolyPhen 2 Score 0.808 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000032775
Gene: ENSMUSG00000030556
AA Change: T54K

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: T54K

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000052177
Gene: ENSMUSG00000030556
AA Change: T54K

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

possibly damaging
Transcript: ENSMUST00000187953
AA Change: T54K

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000189836
AA Change: T54K

PolyPhen 2 Score 0.646 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000139606
Gene: ENSMUSG00000030556
AA Change: T54K

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000190276
AA Change: T54K

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000140972
Gene: ENSMUSG00000030556
AA Change: T54K

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

possibly damaging
Transcript: ENSMUST00000191035
AA Change: T54K

PolyPhen 2 Score 0.728 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000140382
Gene: ENSMUSG00000030556
AA Change: T54K

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: ENSMUST00000209153

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.0%
20x: 91.5%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	T	C	12: 71,197,018 (GRCm39)	V197A	possibly damaging	Het
9230109A22Rik	T	C	15: 25,139,176 (GRCm39)		noncoding transcript	Het
Acbd3	A	G	1: 180,572,703 (GRCm39)	N321S	probably benign	Het
Actr3b	T	C	5: 26,054,156 (GRCm39)		probably null	Het
Aldh5a1	T	C	13: 25,111,555 (GRCm39)	D124G	probably benign	Het
Arhgap35	G	A	7: 16,295,874 (GRCm39)	R1064W	possibly damaging	Het
Arhgef9	T	A	X: 94,125,142 (GRCm39)	I225F	probably damaging	Het
Arl16	T	C	11: 120,357,587 (GRCm39)	T43A	probably damaging	Het
Camsap3	T	C	8: 3,653,485 (GRCm39)	W409R	probably damaging	Het
Cfap43	T	A	19: 47,885,655 (GRCm39)	H320L	probably damaging	Het
Chac2	T	A	11: 30,927,496 (GRCm39)	N141I	probably damaging	Het
Chtf18	C	A	17: 25,944,913 (GRCm39)	G211C	probably damaging	Het
Cplane1	A	G	15: 8,299,129 (GRCm39)	K3106E	unknown	Het
Cwf19l1	T	A	19: 44,115,826 (GRCm39)	Y201F	probably benign	Het
Dcun1d1	A	T	3: 35,973,153 (GRCm39)	L114*	probably null	Het
Fdps	A	T	3: 89,002,350 (GRCm39)	H249Q	probably benign	Het
Fhip1a	T	A	3: 85,573,136 (GRCm39)	T938S	probably damaging	Het
Gabrg1	T	A	5: 70,931,756 (GRCm39)	Y329F	probably damaging	Het
Kctd8	T	A	5: 69,497,684 (GRCm39)	I321F	probably damaging	Het
Kdm5b	G	T	1: 134,525,408 (GRCm39)	R299L	possibly damaging	Het
Kif23	T	C	9: 61,833,720 (GRCm39)	T494A	possibly damaging	Het
Kmt2e	A	G	5: 23,678,545 (GRCm39)	H208R	probably damaging	Het
Lipo5	A	T	19: 33,441,995 (GRCm39)		probably null	Het
Luc7l2	G	A	6: 38,575,754 (GRCm39)		probably null	Het
Man2a2	A	G	7: 80,008,681 (GRCm39)	F899L	probably benign	Het
Myo9b	T	C	8: 71,786,002 (GRCm39)	I633T	probably damaging	Het
Nynrin	A	T	14: 56,107,835 (GRCm39)	I981F	possibly damaging	Het
Or5an1c	A	T	19: 12,218,612 (GRCm39)	S138T	probably damaging	Het
Or8g28	A	G	9: 39,169,695 (GRCm39)	I91T	possibly damaging	Het
Pank1	A	G	19: 34,855,084 (GRCm39)		probably null	Het
Phc2	C	T	4: 128,637,336 (GRCm39)	A47V	probably damaging	Het
Plekhs1	A	G	19: 56,466,954 (GRCm39)	R262G	possibly damaging	Het
Pnp2	C	A	14: 51,201,914 (GRCm39)	P300Q	possibly damaging	Het
Polq	T	A	16: 36,849,780 (GRCm39)	S345T	possibly damaging	Het
Prag1	A	G	8: 36,570,958 (GRCm39)	T514A	probably benign	Het
Psmd5	T	C	2: 34,760,758 (GRCm39)		probably null	Het
Rfx6	T	G	10: 51,599,221 (GRCm39)		probably null	Het
Rhbdd2	G	A	5: 135,664,903 (GRCm39)	C78Y	probably damaging	Het
Rnf157	G	T	11: 116,245,477 (GRCm39)	P313T	probably damaging	Het
Ryr2	A	G	13: 11,602,202 (GRCm39)	L4560P	probably damaging	Het
Scai	A	T	2: 38,996,990 (GRCm39)	M268K	possibly damaging	Het
Scd3	A	T	19: 44,230,245 (GRCm39)	T343S	probably benign	Het
Scimp	A	T	11: 70,682,423 (GRCm39)	S98T	probably benign	Het
Sfrp2	A	G	3: 83,680,461 (GRCm39)	N207S	probably benign	Het
Shf	G	A	2: 122,199,163 (GRCm39)	P51S	probably damaging	Het
Sis	T	C	3: 72,828,475 (GRCm39)	Y1200C	probably damaging	Het
Sp1	T	A	15: 102,317,511 (GRCm39)	S343R	possibly damaging	Het
Spata31d1a	A	T	13: 59,849,069 (GRCm39)	C1020S	possibly damaging	Het
Spink5	A	G	18: 44,122,486 (GRCm39)	N317S	possibly damaging	Het
Sptbn2	A	G	19: 4,776,624 (GRCm39)	D224G	probably damaging	Het
St8sia3	T	C	18: 64,402,703 (GRCm39)	I114T	probably damaging	Het
Zscan5b	C	A	7: 6,242,162 (GRCm39)	H460Q	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
R0652: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
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'- AAGGTCACTTTCCTGCATATCCG -3'
(R):5'- ACAAGATGTAGTGCGACAGC -3'

Sequencing Primer
(F):5'- CGTTCTGTAGCCTAACTGGATGAAC -3'
(R):5'- AGCACTTCCGGTTGGACATG -3'

Posted On

2014-06-23