Incidental Mutation 'R2110:Ecm1'
ID 232439
Institutional Source Beutler Lab
Gene Symbol Ecm1
Ensembl Gene ENSMUSG00000028108
Gene Name extracellular matrix protein 1
Synonyms p85
MMRRC Submission 040114-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.190) question?
Stock # R2110 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 95641459-95646880 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 95643254 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Threonine at position 349 (A349T)
Ref Sequence ENSEMBL: ENSMUSP00000112665 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029752] [ENSMUST00000029753] [ENSMUST00000074339] [ENSMUST00000117507] [ENSMUST00000123143] [ENSMUST00000128885] [ENSMUST00000137912] [ENSMUST00000196077] [ENSMUST00000199464] [ENSMUST00000153026] [ENSMUST00000163530] [ENSMUST00000131376] [ENSMUST00000147217]
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 benign
Transcript: ENSMUST00000029753
AA Change: A348T

PolyPhen 2 Score 0.135 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000029753
Gene: ENSMUSG00000028108
AA Change: A348T

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 benign
Transcript: ENSMUST00000117507
AA Change: A349T

PolyPhen 2 Score 0.135 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000112665
Gene: ENSMUSG00000028108
AA Change: A349T

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: ENSMUST00000144958
Predicted Effect noncoding transcript
Transcript: ENSMUST00000183853
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155815
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199869
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200376
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: 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: ENSMUST00000199464
SMART Domains Protein: ENSMUSP00000143328
Gene: ENSMUSG00000028107

DomainStartEndE-ValueType
Pfam:TGS 66 126 1.1e-13 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000153026
SMART Domains Protein: ENSMUSP00000114747
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 230 1.3e-100 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: ENSMUST00000131376
SMART Domains Protein: ENSMUSP00000114659
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 295 4.2e-146 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000147217
SMART Domains Protein: ENSMUSP00000115524
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 80 5.2e-40 PFAM
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.0%
Validation Efficiency
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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9330161L09Rik T C 12: 103,373,848 (GRCm39) probably benign Het
Ablim1 T C 19: 57,032,245 (GRCm39) D638G possibly damaging Het
Adam1b A G 5: 121,638,777 (GRCm39) probably benign Het
Aim2 T C 1: 173,287,279 (GRCm39) M93T probably benign Het
Alpk2 T C 18: 65,440,151 (GRCm39) E414G possibly damaging Het
Ap1b1 T C 11: 4,965,613 (GRCm39) F51L probably damaging Het
Bard1 T A 1: 71,114,550 (GRCm39) K144* probably null Het
Begain G T 12: 108,999,843 (GRCm39) Y514* probably null Het
Ccdc186 A T 19: 56,788,574 (GRCm39) I545N possibly damaging Het
Cfap251 G A 5: 123,392,438 (GRCm39) probably benign Het
Cfap43 T C 19: 47,824,197 (GRCm39) Y58C probably damaging Het
Cfap54 A T 10: 92,722,229 (GRCm39) D2437E unknown Het
Chd2 A G 7: 73,079,735 (GRCm39) S1722P probably benign Het
Clec5a C T 6: 40,562,137 (GRCm39) G9E probably damaging Het
Cog4 A G 8: 111,585,214 (GRCm39) Y292C possibly damaging Het
Col3a1 C T 1: 45,369,305 (GRCm39) P331S unknown Het
Ctsk T C 3: 95,413,988 (GRCm39) I245T probably benign Het
Dthd1 T C 5: 62,979,251 (GRCm39) Y304H probably damaging Het
Dthd1 T C 5: 63,000,222 (GRCm39) S515P probably damaging Het
Dtx2 C T 5: 136,059,431 (GRCm39) S493F probably damaging Het
Eci2 A G 13: 35,174,699 (GRCm39) probably null Het
Efemp2 A G 19: 5,525,190 (GRCm39) E32G probably damaging Het
Flt4 C A 11: 49,516,131 (GRCm39) T78K probably benign Het
Foxg1 A G 12: 49,431,708 (GRCm39) probably benign Het
Fv1 T C 4: 147,954,619 (GRCm39) V395A possibly damaging Het
Gcfc2 C A 6: 81,900,759 (GRCm39) D24E probably benign Het
Gpha2 T G 19: 6,277,532 (GRCm39) V96G probably damaging Het
Gse1 A G 8: 121,293,719 (GRCm39) Y228C probably damaging Het
Hmgxb3 T C 18: 61,288,458 (GRCm39) R470G possibly damaging Het
Ildr1 A G 16: 36,542,341 (GRCm39) E247G probably damaging Het
Ktn1 T A 14: 47,931,345 (GRCm39) M646K possibly damaging Het
Lrrc37a T A 11: 103,388,648 (GRCm39) H2259L unknown Het
Map1b A T 13: 99,567,629 (GRCm39) H1697Q unknown Het
Mdn1 A G 4: 32,700,409 (GRCm39) E1456G probably damaging Het
Mta1 C T 12: 113,095,248 (GRCm39) T467I probably damaging Het
Nav1 C T 1: 135,376,742 (GRCm39) R1694Q probably damaging Het
Ncoa5 C A 2: 164,854,838 (GRCm39) D95Y possibly damaging Het
Nfatc1 A T 18: 80,678,879 (GRCm39) C836* probably null Het
Nr3c2 T C 8: 77,635,156 (GRCm39) S86P possibly damaging Het
Nup153 A G 13: 46,837,404 (GRCm39) S1273P probably benign Het
Or8g52 G A 9: 39,631,018 (GRCm39) R165Q probably benign Het
Pcsk5 C A 19: 17,450,423 (GRCm39) G1142C probably damaging Het
Pgghg A G 7: 140,523,453 (GRCm39) D244G possibly damaging Het
Polr1has T C 17: 37,276,336 (GRCm39) V306A possibly damaging Het
Ppargc1b G A 18: 61,444,321 (GRCm39) P297S probably benign Het
Rad52 A T 6: 119,897,855 (GRCm39) Q356L possibly damaging Het
Rhpn1 T A 15: 75,585,083 (GRCm39) F507I probably damaging Het
Rhpn2 T C 7: 35,076,433 (GRCm39) M328T probably benign Het
Rnf19a T C 15: 36,254,665 (GRCm39) I298V possibly damaging Het
Rwdd2a T C 9: 86,456,184 (GRCm39) V120A probably benign Het
Scml2 G T X: 160,014,442 (GRCm39) E566D possibly damaging Het
Serpina3a G A 12: 104,082,481 (GRCm39) A85T probably damaging Het
Slc16a11 G A 11: 70,106,146 (GRCm39) G80D probably damaging Het
Slc5a5 A T 8: 71,342,395 (GRCm39) probably null Het
Sparcl1 T A 5: 104,236,289 (GRCm39) Q488L probably damaging Het
Spg21 T A 9: 65,391,711 (GRCm39) probably null Het
Spopfm2 A G 3: 94,082,834 (GRCm39) S326P probably damaging Het
Sry T C Y: 2,662,901 (GRCm39) H253R unknown Het
Swt1 A G 1: 151,279,636 (GRCm39) S391P probably damaging Het
Uhrf2 A G 19: 30,033,888 (GRCm39) Y200C probably damaging Het
Utp15 T C 13: 98,391,493 (GRCm39) H248R probably damaging Het
Utp20 A G 10: 88,603,313 (GRCm39) probably null Het
Vcan T A 13: 89,841,422 (GRCm39) D414V probably damaging Het
Vmn1r56 A T 7: 5,199,179 (GRCm39) M146K probably damaging Het
Zfp143 A T 7: 109,685,453 (GRCm39) K399N probably damaging Het
Zfp516 A G 18: 82,975,536 (GRCm39) D578G probably damaging Het
Zfp90 G A 8: 107,152,120 (GRCm39) C611Y 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
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
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'- CACAACGGACGGATGGATTG -3'
(R):5'- CGATTCTCTTGCTTCCAGAAGG -3'

Sequencing Primer
(F):5'- CGGACAGTCACAAGCAGACG -3'
(R):5'- GAAGCTCCTCGCCCAGAC -3'
Posted On 2014-09-18