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Gene

ECM1

extracellular matrix protein 1

Summary

Cytogenetic location
1q21.2
Coordinates
Chromosome 1: 150,508,109–150,513,789 (GRCh38)
Exons
10 exons across 5.7 kb
Protein
540 amino acids
Inheritance
Autosomal recessive
MANE Select transcript
ENST00000369047.9NM_004425.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Lipoid Proteinosis

    • Autosomal recessive

      An ECM1 disorder with a hoarse voice from infancy, beaded papules on the eyelids, skin scarring, and sometimes calcification in the brain that can cause seizures.

      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Diagnosis can explain long-standing hoarseness and prompts assessment for seizures.

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How ECM1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 1, with a bracket where ECM1 sits. ECM1 and 25 genes near it on chromosome 1, from 150,010,949 to 151,010,948.Chromosome 11q21.2p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44150.2 Mb150.4 Mb150.6 Mb150.8 Mb151 MbVPS45: 150,067,279–150,145,329, forward strandVPS45PLEKHO1: 150,149,183–150,164,720, forward strandPLEKHO1ANP32E: 150,217,463–150,236,202, reverse strandANP32ECA14: 150,257,069–150,265,078, forward strandAPH1A: 150,265,042–150,269,580, reverse strandAPH1AC1orf54: 150,268,034–150,281,744, forward strandC1orf54CIART: 150,282,527–150,287,093, forward strandCIARTMRPS21: 150,293,848–150,309,828, forward strandMRPS21PRPF3: 150,321,476–150,353,341, forward strandPRPF3RPRD2: 150,363,091–150,476,999, forward strandRPRD2TARS2: 150,487,325–150,507,614, forward strandTARS2ECM1: 150,508,109–150,513,789, forward strandECM1ADAMTSL4: 150,549,369–150,560,937, forward strandADAMTSL4MCL1: 150,560,895–150,579,738, reverse strandMCL1ENSA: 150,599,671–150,629,633, reverse strandENSAGOLPH3L: 150,638,727–150,697,222, reverse strandGOLPH3LHORMAD1: 150,698,059–150,720,895, reverse strandHORMAD1CTSS: 150,730,079–150,765,957, reverse strandCTSSCTSK: 150,794,880–150,809,577, reverse strandCTSKARNT: 150,808,617–150,876,771, reverse strandARNTCTXND2: 150,887,136–150,913,292, forward strandCTXND2SETDB1: 150,926,263–150,964,748, forward strandSETDB1CERS2: 150,959,099–150,977,396, reverse strandCERS2ANXA9: 150,981,321–150,996,077, forward strandANXA9MINDY1: 150,995,125–151,008,376, reverse strandMINDY1PRUNE1: 151,008,408–151,035,714, forward strandPRUNE1Diagram of ECM1: 10 exons on the forward strand of chromosome 1Exon 1: 2 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 4: 1 known disease-causing siteExon 6: 4 known disease-causing sitesExon 7: 5 known disease-causing sitesExon 8: 4 known disease-causing sitesExon 10: 1 known disease-causing siteExon 1: 150,508,109–150,508,279, 171 basesExon 2: 150,509,531–150,509,581, 51 basesExon 3: 150,509,661–150,509,762, 102 basesExon 4: 150,509,922–150,510,002, 81 basesExon 5: 150,510,102–150,510,182, 81 basesExon 6: 150,510,876–150,511,198, 323 basesExon 7: 150,511,457–150,511,831, 375 basesExon 8: 150,512,352–150,512,572, 221 basesExon 9: 150,512,725–150,512,812, 88 basesExon 10: 150,513,237–150,513,789, 553 bases123456789105′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2 kb of the gene's 5.7 kb; 1,623 of those bases code for the protein.

How a genome test reads ECM1

22

positions in ECM1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 5.7 kb of ECM1, introns included, not only the 2 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). ECM1 gene: extracellular matrix protein 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/ecm1

Vancouver

Dante Labs. ECM1 gene: extracellular matrix protein 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ecm1

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