Mutagenetix > Incidental Mutation

Incidental Mutation 'R1484:Ecm1'

163287

Institutional Source

Beutler Lab

Gene Symbol

Ecm1

Ensembl Gene

ENSMUSG00000028108

Gene Name

extracellular matrix protein 1

Synonyms

p85

MMRRC Submission

039537-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.190) question?

Stock #

R1484 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

95641459-95646880 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 95643275 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 342 (R342C)

Ref Sequence

ENSEMBL: ENSMUSP00000112665 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029752] [ENSMUST00000029753] [ENSMUST00000074339] [ENSMUST00000117507] [ENSMUST00000123143] [ENSMUST00000128885] [ENSMUST00000131376] [ENSMUST00000163530] [ENSMUST00000196077] [ENSMUST00000147217] [ENSMUST00000199464] [ENSMUST00000137912] [ENSMUST00000153026]

AlphaFold

Q61508

Predicted Effect

probably benign
Transcript: ENSMUST00000029752

SMART Domains

Protein: ENSMUSP00000029752
Gene: ENSMUSG00000028107

Domain	Start	End	E-Value	Type
Pfam:TGS	66	126	5.6e-14	PFAM
tRNA_SAD	233	282	1.15e-10	SMART
Pfam:tRNA-synt_2b	400	608	2.4e-32	PFAM
Pfam:HGTP_anticodon	620	711	1.5e-18	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000029753
AA Change: R341C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000029753
Gene: ENSMUSG00000028108
AA Change: R341C

Domain	Start	End	E-Value	Type
Pfam:ECM1	1	558	N/A	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000074339

SMART Domains

Protein: ENSMUSP00000073946
Gene: ENSMUSG00000028107

Domain	Start	End	E-Value	Type
Pfam:TGS	66	126	1.3e-15	PFAM
tRNA_SAD	233	282	1.15e-10	SMART
Pfam:tRNA-synt_2b	336	519	2.8e-39	PFAM
Pfam:HGTP_anticodon	594	685	5.4e-20	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000117507
AA Change: R342C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000112665
Gene: ENSMUSG00000028108
AA Change: R342C

Domain	Start	End	E-Value	Type
Pfam:ECM1	1	559	N/A	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000123143

SMART Domains

Protein: ENSMUSP00000120300
Gene: ENSMUSG00000028108

Domain	Start	End	E-Value	Type
Pfam:ECM1	1	266	4.4e-132	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000128885

SMART Domains

Protein: ENSMUSP00000120820
Gene: ENSMUSG00000028108

Domain	Start	End	E-Value	Type
Pfam:ECM1	1	251	1.5e-135	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000131376

SMART Domains

Protein: ENSMUSP00000114659
Gene: ENSMUSG00000028108

Domain	Start	End	E-Value	Type
Pfam:ECM1	1	295	4.2e-146	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155815

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144958

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183853

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199869

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200376

Predicted Effect

probably benign
Transcript: ENSMUST00000163530

SMART Domains

Protein: ENSMUSP00000130269
Gene: ENSMUSG00000028107

Domain	Start	End	E-Value	Type
Pfam:TGS	66	126	2.6e-15	PFAM
tRNA_SAD	152	201	1.15e-10	SMART
Pfam:tRNA-synt_2b	255	438	8.6e-40	PFAM
Pfam:HGTP_anticodon	539	630	1.6e-20	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000196077

SMART Domains

Protein: ENSMUSP00000143722
Gene: ENSMUSG00000028107

Domain	Start	End	E-Value	Type
Pfam:TGS	65	125	5e-13	PFAM
tRNA_SAD	232	264	7.5e-5	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000147217

SMART Domains

Protein: ENSMUSP00000115524
Gene: ENSMUSG00000028108

Domain	Start	End	E-Value	Type
Pfam:ECM1	1	80	5.2e-40	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000199464

SMART Domains

Protein: ENSMUSP00000143328
Gene: ENSMUSG00000028107

Domain	Start	End	E-Value	Type
Pfam:TGS	66	126	1.1e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000137912

SMART Domains

Protein: ENSMUSP00000122243
Gene: ENSMUSG00000028108

Domain	Start	End	E-Value	Type
Pfam:ECM1	1	140	1.8e-39	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153026

SMART Domains

Protein: ENSMUSP00000114747
Gene: ENSMUSG00000028108

Domain	Start	End	E-Value	Type
Pfam:ECM1	1	230	1.3e-100	PFAM

Meta Mutation Damage Score

0.2379

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.5%
20x: 93.4%

Validation Efficiency

97% (85/88)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a soluble protein that is involved in endochondral bone formation, angiogenesis, and tumor biology. It also interacts with a variety of extracellular and structural proteins, contributing to the maintenance of skin integrity and homeostasis. Mutations in this gene are associated with lipoid proteinosis disorder (also known as hyalinosis cutis et mucosae or Urbach-Wiethe disease) that is characterized by generalized thickening of skin, mucosae and certain viscera. Alternatively spliced transcript variants encoding distinct isoforms have been described for this gene. [provided by RefSeq, Feb 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit auto-inflammatory disease and do not survive beyond 6 to 8 weeks of age. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930584F24Rik	A	T	5: 26,684,776 (GRCm39)		noncoding transcript	Het
Acvr1	A	T	2: 58,369,901 (GRCm39)	V36E	probably damaging	Het
Aldh4a1	A	G	4: 139,370,758 (GRCm39)	I414V	probably benign	Het
Alox5	C	T	6: 116,431,128 (GRCm39)	C100Y	probably damaging	Het
Ano5	T	A	7: 51,216,068 (GRCm39)	D348E	probably damaging	Het
Arhgap30	G	A	1: 171,230,839 (GRCm39)	V199M	probably damaging	Het
Arl13b	T	A	16: 62,626,999 (GRCm39)	Q234L	probably benign	Het
Atxn1	C	A	13: 45,711,052 (GRCm39)	E627*	probably null	Het
Bend3	T	C	10: 43,386,197 (GRCm39)	F197L	probably benign	Het
Brca1	A	T	11: 101,420,638 (GRCm39)	V190E	possibly damaging	Het
Brpf1	T	C	6: 113,292,096 (GRCm39)	W381R	probably damaging	Het
Brwd1	A	C	16: 95,829,491 (GRCm39)		probably null	Het
C1s2	T	C	6: 124,602,604 (GRCm39)	I530V	possibly damaging	Het
C2cd3	C	T	7: 100,089,397 (GRCm39)	R1638W	probably damaging	Het
Capns1	T	A	7: 29,893,511 (GRCm39)		probably benign	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,619,782 (GRCm39)		probably benign	Het
Cep126	G	A	9: 8,100,554 (GRCm39)	T660I	possibly damaging	Het
Cep295	A	C	9: 15,246,080 (GRCm39)	I744R	probably damaging	Het
Chd3	T	C	11: 69,250,725 (GRCm39)	E668G	probably benign	Het
Chek2	A	G	5: 110,996,553 (GRCm39)	T172A	probably damaging	Het
Col6a4	A	G	9: 105,890,501 (GRCm39)		probably null	Het
Coq3	G	A	4: 21,900,291 (GRCm39)	V173I	probably benign	Het
Cyp4x1	A	T	4: 114,970,098 (GRCm39)	I343N	probably damaging	Het
Dnah7b	T	A	1: 46,176,703 (GRCm39)	D774E	probably benign	Het
Dnai3	T	C	3: 145,802,996 (GRCm39)	D65G	probably benign	Het
Esrra	T	C	19: 6,890,197 (GRCm39)	Y209C	probably damaging	Het
Gpr149	A	T	3: 62,502,592 (GRCm39)	D421E	probably benign	Het
Gpr15	T	C	16: 58,538,937 (GRCm39)	N51D	probably damaging	Het
Gpr156	T	C	16: 37,812,558 (GRCm39)	V298A	probably damaging	Het
Hmcn2	G	A	2: 31,236,507 (GRCm39)	G350D	probably damaging	Het
Ifih1	A	T	2: 62,440,902 (GRCm39)	N421K	probably benign	Het
Ilvbl	C	A	10: 78,412,564 (GRCm39)	T95K	probably damaging	Het
Itgb4	T	A	11: 115,890,625 (GRCm39)	D1104E	probably benign	Het
Katnip	C	A	7: 125,415,743 (GRCm39)		probably benign	Het
Lipf	A	T	19: 33,942,180 (GRCm39)	M37L	probably benign	Het
Lyst	T	A	13: 13,852,775 (GRCm39)	N2258K	probably benign	Het
Moxd1	A	G	10: 24,099,758 (GRCm39)	Y86C	probably damaging	Het
Muc5ac	T	C	7: 141,367,629 (GRCm39)		probably null	Het
Myo16	G	A	8: 10,610,145 (GRCm39)	R1162H	probably damaging	Het
Myo5c	A	T	9: 75,208,092 (GRCm39)	N1609Y	probably damaging	Het
Nbeal1	T	C	1: 60,240,098 (GRCm39)	F155L	probably damaging	Het
Nek4	A	T	14: 30,704,290 (GRCm39)	M602L	possibly damaging	Het
Nek9	A	G	12: 85,348,622 (GRCm39)	S971P	probably damaging	Het
Nfya	A	T	17: 48,700,570 (GRCm39)		probably benign	Het
Nrxn3	A	T	12: 89,221,547 (GRCm39)	N442I	probably damaging	Het
Nup42	A	C	5: 24,383,075 (GRCm39)	K200N	probably benign	Het
Or1e26	T	A	11: 73,480,187 (GRCm39)	I126L	possibly damaging	Het
Or4c111	G	A	2: 88,843,713 (GRCm39)	R232*	probably null	Het
Or7g32	G	A	9: 19,389,423 (GRCm39)	T38I	probably damaging	Het
Pcdh15	T	A	10: 74,126,833 (GRCm39)	I304N	probably damaging	Het
Pigo	G	C	4: 43,024,779 (GRCm39)	P107A	probably damaging	Het
Plce1	C	T	19: 38,693,783 (GRCm39)	Q769*	probably null	Het
Plin2	C	T	4: 86,575,481 (GRCm39)	R356H	probably benign	Het
Ppp1r9a	G	T	6: 5,113,712 (GRCm39)	E739*	probably null	Het
Ppp3cc	G	T	14: 70,478,397 (GRCm39)	N268K	probably damaging	Het
Prkag3	T	A	1: 74,779,919 (GRCm39)	D472V	probably damaging	Het
Ptch2	A	T	4: 116,968,046 (GRCm39)	D846V	probably damaging	Het
Rhob	A	T	12: 8,549,388 (GRCm39)	M82K	probably damaging	Het
Rps6kc1	T	A	1: 190,531,672 (GRCm39)	R777W	possibly damaging	Het
Sap130	T	A	18: 31,844,380 (GRCm39)	V850E	probably damaging	Het
Sema3a	T	G	5: 13,523,407 (GRCm39)	N125K	probably damaging	Het
Sema5a	A	G	15: 32,460,431 (GRCm39)	D64G	probably damaging	Het
Sgo2b	T	A	8: 64,384,507 (GRCm39)	D163V	possibly damaging	Het
Slc15a1	A	T	14: 121,728,651 (GRCm39)	Y31*	probably null	Het
Smchd1	A	T	17: 71,685,252 (GRCm39)	M1392K	probably benign	Het
Sobp	T	A	10: 43,036,827 (GRCm39)	N37I	probably damaging	Het
Spock3	G	T	8: 63,673,739 (GRCm39)	C142F	probably damaging	Het
Stx6	A	C	1: 155,053,650 (GRCm39)	S86R	probably benign	Het
Sult2a4	C	A	7: 13,643,726 (GRCm39)	M280I	probably benign	Het
Synm	A	T	7: 67,386,080 (GRCm39)	D527E	probably damaging	Het
Tax1bp1	C	T	6: 52,710,305 (GRCm39)	R195W	probably damaging	Het
Themis2	A	T	4: 132,519,796 (GRCm39)	N76K	possibly damaging	Het
Tmem8b	A	G	4: 43,690,234 (GRCm39)	T890A	probably benign	Het
Traf7	T	A	17: 24,730,785 (GRCm39)	H366L	possibly damaging	Het
Trim30c	A	T	7: 104,032,459 (GRCm39)	V289D	probably benign	Het
Tsr1	T	A	11: 74,792,914 (GRCm39)	D407E	probably damaging	Het
Ubap2	G	T	4: 41,235,593 (GRCm39)	A33E	probably damaging	Het
Unc13d	C	A	11: 115,964,701 (GRCm39)	R255L	possibly damaging	Het
Ush2a	G	T	1: 188,542,534 (GRCm39)	G3367*	probably null	Het
Vmn1r229	T	C	17: 21,034,791 (GRCm39)	L12P	probably damaging	Het
Vmn2r27	C	A	6: 124,177,474 (GRCm39)	G510V	probably damaging	Het
Vps4b	T	C	1: 106,707,712 (GRCm39)	E257G	probably damaging	Het
Vps72	T	C	3: 95,026,462 (GRCm39)	S136P	probably damaging	Het
Wdr36	T	C	18: 32,976,938 (GRCm39)	I181T	possibly damaging	Het
Wfikkn1	C	T	17: 26,096,765 (GRCm39)	A520T	probably benign	Het

Other mutations in Ecm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01634:Ecm1	APN	3	95,642,211 (GRCm39)	missense	probably damaging	1.00
IGL01686:Ecm1	APN	3	95,643,376 (GRCm39)	missense	probably benign
IGL01807:Ecm1	APN	3	95,643,891 (GRCm39)	missense	probably damaging	1.00
IGL01862:Ecm1	APN	3	95,641,586 (GRCm39)	missense	probably benign	0.08
IGL02006:Ecm1	APN	3	95,641,557 (GRCm39)	missense	probably damaging	0.98
IGL02134:Ecm1	APN	3	95,643,499 (GRCm39)	missense	probably damaging	1.00
IGL02210:Ecm1	APN	3	95,643,289 (GRCm39)	missense	probably damaging	0.97
IGL02813:Ecm1	APN	3	95,644,098 (GRCm39)	missense	probably damaging	0.99
IGL02959:Ecm1	APN	3	95,644,989 (GRCm39)	missense	probably damaging	1.00
R0362:Ecm1	UTSW	3	95,644,369 (GRCm39)	missense	possibly damaging	0.93
R0963:Ecm1	UTSW	3	95,643,900 (GRCm39)	missense	possibly damaging	0.95
R1181:Ecm1	UTSW	3	95,642,662 (GRCm39)	missense	possibly damaging	0.85
R1230:Ecm1	UTSW	3	95,642,738 (GRCm39)	splice site	probably null
R1483:Ecm1	UTSW	3	95,643,275 (GRCm39)	missense	probably damaging	1.00
R1559:Ecm1	UTSW	3	95,643,275 (GRCm39)	missense	probably damaging	1.00
R1561:Ecm1	UTSW	3	95,643,275 (GRCm39)	missense	probably damaging	1.00
R1562:Ecm1	UTSW	3	95,643,275 (GRCm39)	missense	probably damaging	1.00
R1590:Ecm1	UTSW	3	95,643,275 (GRCm39)	missense	probably damaging	1.00
R1591:Ecm1	UTSW	3	95,643,275 (GRCm39)	missense	probably damaging	1.00
R2110:Ecm1	UTSW	3	95,643,254 (GRCm39)	missense	probably benign	0.14
R3236:Ecm1	UTSW	3	95,642,158 (GRCm39)	missense	possibly damaging	0.71
R3897:Ecm1	UTSW	3	95,643,298 (GRCm39)	missense	probably damaging	0.99
R4084:Ecm1	UTSW	3	95,641,676 (GRCm39)	missense	probably damaging	0.98
R4770:Ecm1	UTSW	3	95,645,273 (GRCm39)	unclassified	probably benign
R4985:Ecm1	UTSW	3	95,643,415 (GRCm39)	missense	possibly damaging	0.55
R5506:Ecm1	UTSW	3	95,643,169 (GRCm39)	missense	probably benign	0.00
R5861:Ecm1	UTSW	3	95,643,909 (GRCm39)	missense	probably damaging	1.00
R7472:Ecm1	UTSW	3	95,642,632 (GRCm39)	missense	possibly damaging	0.93
R7678:Ecm1	UTSW	3	95,643,494 (GRCm39)	missense	probably damaging	0.97
R7704:Ecm1	UTSW	3	95,643,843 (GRCm39)	missense	probably damaging	0.99
R7864:Ecm1	UTSW	3	95,641,689 (GRCm39)	missense	probably benign	0.09
Z1088:Ecm1	UTSW	3	95,642,188 (GRCm39)	missense	probably benign
Z1176:Ecm1	UTSW	3	95,642,188 (GRCm39)	missense	probably benign
Z1177:Ecm1	UTSW	3	95,642,188 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ACTTGGATGACAGACACAACGGAC -3'
(R):5'- ATGCAATGACCCAATTTTGTGAGGC -3'

Sequencing Primer
(F):5'- acacaacggacggatgg -3'
(R):5'- AGGCCGAATTCTCTGTCAAG -3'

Posted On

2014-03-28