Mutagenetix > Incidental Mutation

Incidental Mutation 'R5980:Lysmd1'

481364

Institutional Source

Beutler Lab

Gene Symbol

Lysmd1

Ensembl Gene

ENSMUSG00000053769

Gene Name

LysM, putative peptidoglycan-binding, domain containing 1

Synonyms

2610022K04Rik

MMRRC Submission

044162-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.087) question?

Stock #

R5980 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

95041399-95046829 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 95045219 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 155 (D155V)

Ref Sequence

ENSEMBL: ENSMUSP00000067811 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000013851] [ENSMUST00000066386] [ENSMUST00000172572] [ENSMUST00000173462]

AlphaFold

Q9D0E3

Predicted Effect

probably benign
Transcript: ENSMUST00000013851

SMART Domains

Protein: ENSMUSP00000013851
Gene: ENSMUSG00000013707

Domain	Start	End	E-Value	Type
Pfam:DUF758	4	182	2.4e-75	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000066386
AA Change: D155V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000067811
Gene: ENSMUSG00000053769
AA Change: D155V

Domain	Start	End	E-Value	Type
low complexity region	10	19	N/A	INTRINSIC
LysM	41	85	2.58e-7	SMART
low complexity region	100	108	N/A	INTRINSIC
low complexity region	117	132	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000172572

SMART Domains

Protein: ENSMUSP00000134337
Gene: ENSMUSG00000092607

Domain	Start	End	E-Value	Type
Pfam:zf-SCNM1	44	70	7.6e-19	PFAM
low complexity region	133	148	N/A	INTRINSIC
low complexity region	172	179	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000173462

SMART Domains

Protein: ENSMUSP00000133769
Gene: ENSMUSG00000092607

Domain	Start	End	E-Value	Type
Blast:ZnF_C2H2	42	68	2e-7	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173527

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174859

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184238

Meta Mutation Damage Score

0.6534

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.2%

Validation Efficiency

96% (50/52)

Allele List at MGI

Other mutations in this stock

Total: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	T	C	6: 128,544,018 (GRCm39)	N508D	possibly damaging	Het
Ago1	C	T	4: 126,354,362 (GRCm39)		probably benign	Het
Apol6	A	T	15: 76,935,219 (GRCm39)	T163S	possibly damaging	Het
Arhgap27	T	C	11: 103,247,095 (GRCm39)	T33A	probably benign	Het
Atg7	C	A	6: 114,657,197 (GRCm39)	F132L	possibly damaging	Het
Cep104	C	A	4: 154,072,930 (GRCm39)	A396E	probably benign	Het
Cers4	T	A	8: 4,568,269 (GRCm39)	C107*	probably null	Het
Cntn6	T	C	6: 104,825,093 (GRCm39)	S878P	probably damaging	Het
Dnah6	T	C	6: 73,158,705 (GRCm39)	K633E	probably benign	Het
Dst	T	A	1: 34,221,972 (GRCm39)	I2592K	probably benign	Het
Ep400	G	A	5: 110,881,595 (GRCm39)		probably benign	Het
Fbn1	A	G	2: 125,157,324 (GRCm39)	C2320R	probably damaging	Het
Gpi1	A	G	7: 33,928,351 (GRCm39)		probably null	Het
Gse1	T	G	8: 120,956,376 (GRCm39)		probably benign	Het
Hid1	G	A	11: 115,241,774 (GRCm39)	T612I	possibly damaging	Het
Ighmbp2	G	T	19: 3,315,295 (GRCm39)	H708Q	probably benign	Het
Igkv10-95	T	C	6: 68,657,573 (GRCm39)	S10P	probably damaging	Het
Igkv14-100	T	C	6: 68,496,009 (GRCm39)	V5A	probably benign	Het
Irgq	G	A	7: 24,232,770 (GRCm39)	G204S	probably damaging	Het
Kansl1	T	C	11: 104,234,463 (GRCm39)	K681R	possibly damaging	Het
Kcnv1	C	A	15: 44,972,810 (GRCm39)	V358L	probably damaging	Het
Lrp2	A	T	2: 69,365,349 (GRCm39)	S275T	probably damaging	Het
Magel2	A	T	7: 62,030,344 (GRCm39)	I1083F	unknown	Het
Mta3	T	A	17: 84,015,834 (GRCm39)	V12D	probably damaging	Het
Mtmr4	T	C	11: 87,494,977 (GRCm39)	I423T	probably damaging	Het
Mup11	A	G	4: 60,616,887 (GRCm39)	Y16H	possibly damaging	Het
Mycbp	G	A	4: 123,804,889 (GRCm39)	V91I	probably benign	Het
Ngly1	A	C	14: 16,270,509 (GRCm38)	Q72P	possibly damaging	Het
Nol4	T	A	18: 23,085,258 (GRCm39)	Q52L	probably damaging	Het
Nrcam	T	C	12: 44,618,416 (GRCm39)	V808A	probably damaging	Het
Or10p22	A	G	10: 128,826,309 (GRCm39)	H176R	probably damaging	Het
Or5ak23	A	T	2: 85,244,509 (GRCm39)	F238Y	probably damaging	Het
Or8k24	A	T	2: 86,216,141 (GRCm39)	L207*	probably null	Het
Pate10	A	C	9: 35,652,911 (GRCm39)	D51A	probably damaging	Het
Pik3c2b	C	A	1: 133,016,046 (GRCm39)	D869E	probably benign	Het
Pom121l2	T	C	13: 22,167,546 (GRCm39)	S606P	probably damaging	Het
Prdm15	G	A	16: 97,613,770 (GRCm39)	R517*	probably null	Het
Ralgapa1	T	A	12: 55,817,401 (GRCm39)		probably null	Het
Saraf	T	A	8: 34,632,541 (GRCm39)	F207I	probably benign	Het
Sema6d	A	G	2: 124,506,628 (GRCm39)	D874G	probably damaging	Het
Sfrp5	A	T	19: 42,190,411 (GRCm39)	L14M	unknown	Het
Sidt1	A	T	16: 44,083,675 (GRCm39)	C485*	probably null	Het
Sptbn4	A	G	7: 27,071,596 (GRCm39)	Y1618H	probably damaging	Het
Syt14	T	C	1: 192,662,716 (GRCm39)	Q127R	possibly damaging	Het
Tbc1d2	C	T	4: 46,629,912 (GRCm39)	G252R	probably benign	Het
Ticrr	G	A	7: 79,310,703 (GRCm39)	A206T	probably damaging	Het
Tmem132d	T	A	5: 127,861,662 (GRCm39)	I820F	probably benign	Het
Trafd1	A	G	5: 121,511,520 (GRCm39)	Y433H	probably damaging	Het
Trim68	A	G	7: 102,328,038 (GRCm39)	V305A	probably damaging	Het
Vmn2r58	T	A	7: 41,514,480 (GRCm39)	Y163F	possibly damaging	Het
Vmn2r83	T	A	10: 79,314,626 (GRCm39)	H291Q	probably benign	Het
Vmn2r95	A	G	17: 18,661,624 (GRCm39)	I457V	probably benign	Het

Other mutations in Lysmd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03069:Lysmd1	APN	3	95,044,945 (GRCm39)	missense	probably damaging	1.00
R2105:Lysmd1	UTSW	3	95,042,285 (GRCm39)	missense	probably damaging	1.00
R2504:Lysmd1	UTSW	3	95,045,708 (GRCm39)	missense	probably benign	0.00
R3849:Lysmd1	UTSW	3	95,045,772 (GRCm39)	missense	probably damaging	1.00
R4785:Lysmd1	UTSW	3	95,042,297 (GRCm39)	missense	probably damaging	1.00
R6592:Lysmd1	UTSW	3	95,045,197 (GRCm39)	missense	probably benign	0.18
R7390:Lysmd1	UTSW	3	95,045,795 (GRCm39)	missense	probably damaging	0.98
R8906:Lysmd1	UTSW	3	95,045,219 (GRCm39)	missense	probably damaging	1.00
R8927:Lysmd1	UTSW	3	95,045,831 (GRCm39)	missense	probably damaging	1.00
R8928:Lysmd1	UTSW	3	95,045,831 (GRCm39)	missense	probably damaging	1.00
R9527:Lysmd1	UTSW	3	95,042,156 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- ATCCTATCAGAGCCCAGAGACTTG -3'
(R):5'- GGAGAAAGGCATCCACTTGC -3'

Sequencing Primer
(F):5'- TCAGAGCCCAGAGACTTGTTTAATGG -3'
(R):5'- ACTTGCCTGTCCTCGGG -3'

Posted On

2017-06-26