Incidental Mutation 'R5506:Ecm1'
ID 484465
Institutional Source Beutler Lab
Gene Symbol Ecm1
Ensembl Gene ENSMUSG00000028108
Gene Name extracellular matrix protein 1
Synonyms p85
MMRRC Submission 043067-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.190) question?
Stock # R5506 (G1)
Quality Score 67
Status Validated
Chromosome 3
Chromosomal Location 95641459-95646880 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 95643169 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 377 (T377I)
Ref Sequence ENSEMBL: ENSMUSP00000112665 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029752] [ENSMUST00000029753] [ENSMUST00000074339] [ENSMUST00000117507] [ENSMUST00000123143] [ENSMUST00000128885] [ENSMUST00000131376] [ENSMUST00000147217] [ENSMUST00000199464] [ENSMUST00000137912] [ENSMUST00000196077] [ENSMUST00000163530] [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 benign
Transcript: ENSMUST00000029753
AA Change: T376I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000029753
Gene: ENSMUSG00000028108
AA Change: T376I

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: T377I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000112665
Gene: ENSMUSG00000028108
AA Change: T377I

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: ENSMUST00000199869
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200376
Predicted Effect noncoding transcript
Transcript: ENSMUST00000183853
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144958
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155815
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
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: 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: 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: ENSMUST00000153026
SMART Domains Protein: ENSMUSP00000114747
Gene: ENSMUSG00000028108

DomainStartEndE-ValueType
Pfam:ECM1 1 230 1.3e-100 PFAM
Meta Mutation Damage Score 0.3837 question?
Coding Region Coverage
  • 1x: 98.3%
  • 3x: 97.3%
  • 10x: 95.4%
  • 20x: 91.4%
Validation Efficiency 100% (53/53)
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik G T 3: 137,773,708 (GRCm39) G966W probably damaging Het
A930009A15Rik G T 10: 115,414,267 (GRCm39) probably null Het
Cant1 G T 11: 118,302,268 (GRCm39) H16Q probably benign Het
Capn3 G T 2: 120,332,901 (GRCm39) V612F probably damaging Het
Cep112 A T 11: 108,555,429 (GRCm39) E141D probably damaging Het
Cept1 A G 3: 106,438,564 (GRCm39) V173A probably benign Het
CN725425 A G 15: 91,120,029 (GRCm39) D50G possibly damaging Het
Cubn A T 2: 13,496,506 (GRCm39) probably null Het
Dnajb12 GC G 10: 59,728,574 (GRCm39) probably null Het
Dpp8 A G 9: 64,985,391 (GRCm39) probably null Het
Exosc8 A G 3: 54,638,600 (GRCm39) probably benign Het
Fasn C T 11: 120,700,336 (GRCm39) D2165N probably benign Het
Gab2 A G 7: 96,952,320 (GRCm39) E571G probably damaging Het
Galnt5 C A 2: 57,889,637 (GRCm39) H412Q probably benign Het
Galr1 T A 18: 82,423,989 (GRCm39) Y96F possibly damaging Het
Garin1b G A 6: 29,319,297 (GRCm39) E34K probably damaging Het
Gnl2 C A 4: 124,949,158 (GRCm39) probably benign Het
H2ac22 A C 13: 21,971,081 (GRCm39) I103S probably damaging Het
H2ax T C 9: 44,246,402 (GRCm39) V115A probably benign Het
Heatr9 T C 11: 83,405,592 (GRCm39) N317S possibly damaging Het
Kndc1 A G 7: 139,507,804 (GRCm39) Y1254C probably damaging Het
Lrp6 A T 6: 134,436,259 (GRCm39) D1302E probably benign Het
Mc2r A T 18: 68,541,019 (GRCm39) Y91* probably null Het
Meis1 T G 11: 18,891,747 (GRCm39) D267A possibly damaging Het
Mki67 T C 7: 135,301,710 (GRCm39) K1108R possibly damaging Het
Mroh2a A G 1: 88,186,386 (GRCm39) S64G probably benign Het
Myh3 T G 11: 66,974,915 (GRCm39) D219E probably damaging Het
Niban2 G A 2: 32,810,994 (GRCm39) V335M probably damaging Het
Or10g1b T C 14: 52,628,084 (GRCm39) I49V probably damaging Het
Or7e166 T C 9: 19,624,570 (GRCm39) L149P possibly damaging Het
Pi4ka A G 16: 17,111,817 (GRCm39) C1553R probably damaging Het
Plekhb1 C A 7: 100,294,150 (GRCm39) probably null Het
Polr3d A T 14: 70,678,199 (GRCm39) D165E possibly damaging Het
Prb1c T C 6: 132,338,819 (GRCm39) N133S unknown Het
Psmb1 A G 17: 15,710,478 (GRCm39) Y24H probably damaging Het
Rab11fip5 A G 6: 85,351,119 (GRCm39) L131P probably damaging Het
Raph1 A T 1: 60,532,657 (GRCm39) probably benign Het
Rmc1 A G 18: 12,322,013 (GRCm39) probably benign Het
Scgb2b27 T G 7: 33,711,484 (GRCm39) probably benign Het
Serpina10 T C 12: 103,592,920 (GRCm39) D264G probably damaging Het
Sftpb A G 6: 72,281,651 (GRCm39) T15A possibly damaging Het
Slc20a1 T C 2: 129,052,739 (GRCm39) F674L probably benign Het
Syne2 A T 12: 75,985,495 (GRCm39) N1648Y probably benign Het
Thsd7a G T 6: 12,332,016 (GRCm39) N1265K possibly damaging Het
Trem2 T C 17: 48,658,802 (GRCm39) L189P probably benign Het
Washc4 A T 10: 83,417,201 (GRCm39) R865S probably damaging Het
Zfp536 A G 7: 37,268,217 (GRCm39) S400P 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
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
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'- ATGCATATGTGGGGTCACG -3'
(R):5'- CCAGAATGGCATGTCCTCAG -3'

Sequencing Primer
(F):5'- GTCACGGGTGGATGAAGTC -3'
(R):5'- ATGTCCTCAGGGCCCCAG -3'
Posted On 2017-07-21