Incidental Mutation 'R1590:Ecm1'
ID 177789
Institutional Source Beutler Lab
Gene Symbol Ecm1
Ensembl Gene ENSMUSG00000028108
Gene Name extracellular matrix protein 1
Synonyms p85
MMRRC Submission 039627-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.190) question?
Stock # R1590 (G1)
Quality Score 164
Status Validated
Chromosome 3
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:ECM1 1 558 N/A PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000074339
SMART Domains Protein: ENSMUSP00000073946
Gene: ENSMUSG00000028107

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:ECM1 1 559 N/A PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000123143
SMART Domains Protein: ENSMUSP00000120300
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 266 4.4e-132 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000128885
SMART Domains Protein: ENSMUSP00000120820
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 251 1.5e-135 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: ENSMUST00000131376
SMART Domains Protein: ENSMUSP00000114659
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 295 4.2e-146 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000163530
SMART Domains Protein: ENSMUSP00000130269
Gene: ENSMUSG00000028107

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:ECM1 1 80 5.2e-40 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000199464
SMART Domains Protein: ENSMUSP00000143328
Gene: ENSMUSG00000028107

DomainStartEndE-ValueType
Pfam:TGS 66 126 1.1e-13 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000137912
SMART Domains Protein: ENSMUSP00000122243
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 140 1.8e-39 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000153026
SMART Domains Protein: ENSMUSP00000114747
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 230 1.3e-100 PFAM
Meta Mutation Damage Score 0.2379 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.0%
  • 20x: 91.4%
Validation Efficiency 97% (69/71)
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: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aamp A G 1: 74,322,370 (GRCm39) S95P probably damaging Het
Ankmy1 T C 1: 92,816,397 (GRCm39) Y239C probably damaging Het
Atp12a T C 14: 56,617,512 (GRCm39) S601P probably damaging Het
Atp1b3 T C 9: 96,225,402 (GRCm39) T89A probably benign Het
B3galt4 G A 17: 34,169,813 (GRCm39) R142C probably damaging Het
Brme1 A T 8: 84,893,715 (GRCm39) Q294L probably benign Het
Btnl2 A T 17: 34,580,114 (GRCm39) I216F possibly damaging Het
Cabs1 A T 5: 88,127,490 (GRCm39) H47L probably damaging Het
Ccdc68 T A 18: 70,073,251 (GRCm39) D66E probably benign Het
Cdc42ep4 T C 11: 113,619,392 (GRCm39) D333G possibly damaging Het
Ckmt1 G A 2: 121,194,003 (GRCm39) D389N possibly damaging Het
Dact1 G T 12: 71,364,349 (GRCm39) V340F probably benign Het
Dnah2 T C 11: 69,412,024 (GRCm39) T246A probably benign Het
Dnah2 A G 11: 69,313,580 (GRCm39) probably null Het
Efcab14 A G 4: 115,613,746 (GRCm39) probably benign Het
Eprs1 A G 1: 185,133,707 (GRCm39) T795A probably damaging Het
Esp36 T A 17: 38,728,202 (GRCm39) E26D possibly damaging Het
Fpr-rs7 T C 17: 20,333,678 (GRCm39) T271A probably benign Het
Fsip2 A T 2: 82,813,131 (GRCm39) H3150L probably benign Het
Gimap7 G A 6: 48,700,953 (GRCm39) V180M probably damaging Het
Gtf3c1 T C 7: 125,275,833 (GRCm39) H531R possibly damaging Het
Herc1 T A 9: 66,399,235 (GRCm39) probably benign Het
Hip1r A G 5: 124,140,203 (GRCm39) Y1061C probably benign Het
Ipo11 T C 13: 107,023,225 (GRCm39) Y420C probably damaging Het
Ipo8 T C 6: 148,712,163 (GRCm39) probably null Het
Itga10 C T 3: 96,559,054 (GRCm39) probably benign Het
Klhl1 A T 14: 96,606,072 (GRCm39) M243K probably damaging Het
Lrp2 A G 2: 69,297,107 (GRCm39) probably null Het
Mag T C 7: 30,601,277 (GRCm39) E439G probably damaging Het
Mcm3ap T A 10: 76,332,375 (GRCm39) F1231I probably benign Het
Mcmdc2 C T 1: 9,986,780 (GRCm39) Q204* probably null Het
Mpl A C 4: 118,301,221 (GRCm39) L548R probably damaging Het
Mrps2 C T 2: 28,359,500 (GRCm39) A119V probably benign Het
Myo18b G A 5: 113,023,132 (GRCm39) Q87* probably null Het
Nfat5 A G 8: 108,020,522 (GRCm39) Y22C probably damaging Het
Nnt T A 13: 119,523,197 (GRCm39) I232L possibly damaging Het
Or2a52 A G 6: 43,144,846 (GRCm39) N285D probably damaging Het
Or8g17 T C 9: 38,930,253 (GRCm39) N195D probably benign Het
Or9s13 G A 1: 92,548,467 (GRCm39) V280M possibly damaging Het
Parp2 C T 14: 51,048,001 (GRCm39) P76S probably benign Het
Pick1 C T 15: 79,129,501 (GRCm39) H169Y probably benign Het
Prtg T A 9: 72,750,089 (GRCm39) F164L probably benign Het
Pygb A G 2: 150,659,583 (GRCm39) D422G possibly damaging Het
Samd9l C A 6: 3,375,761 (GRCm39) C500F probably benign Het
Sbno1 A C 5: 124,522,567 (GRCm39) N1083K possibly damaging Het
Septin7 C T 9: 25,188,900 (GRCm39) S77F probably damaging Het
Slc25a44 A G 3: 88,323,314 (GRCm39) V264A possibly damaging Het
Slco1a8 C T 6: 141,926,598 (GRCm39) S576N probably benign Het
Slf2 G T 19: 44,930,512 (GRCm39) E530* probably null Het
Svs5 A G 2: 164,079,578 (GRCm39) S110P possibly damaging Het
Tmbim7 G T 5: 3,715,338 (GRCm39) probably null Het
Tpgs2 T C 18: 25,273,630 (GRCm39) D177G probably damaging Het
Uba1y T A Y: 826,893 (GRCm39) F516L probably damaging Het
Ulk1 A G 5: 110,943,632 (GRCm39) V211A probably damaging Het
Vmn1r237 T A 17: 21,534,301 (GRCm39) I8N probably damaging Het
Vmn2r103 G T 17: 20,014,496 (GRCm39) M429I probably benign Het
Vmn2r112 T C 17: 22,833,989 (GRCm39) probably null Het
Vmn2r84 T C 10: 130,227,349 (GRCm39) probably null Het
Vwa8 C T 14: 79,145,670 (GRCm39) R116C probably damaging Het
Other mutations in Ecm1
AlleleSourceChrCoordTypePredicted EffectPPH 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
R1484: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
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 2014-04-24