ECM1 p.Cys181Ter
c.542_543insAACCAAATCTGAA · rs766844065 · VCV1803965
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 3.353e-05)
Conditions
1
lipoid proteinosis
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 6 of 10 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
0.00335%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- ECM1
- Protein
- p.Cys181Ter
- Coding
- c.542_543insAACCAAATCTGAA
- MANE Select
- NM_004425
- dbSNP
- rs766844065
- Type
- Insertion
- Location
- chr1:150511032 (GRCh38)
- Gene constraint
- LOEUF 1.051 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.05
- Residue 181
- the '2 x approximate repeats' region
Similar variants
- ECM1 p.Cys181fs Likely pathogenic ★ same residue
- ECM1 p.Asn404Ter Pathogenic ★ same condition
- ECM1 p.Arg254Ter Pathogenic ★★ same condition
- ECM1 p.Arg416Ter Pathogenic/Likely pathogenic ★★ same condition
- ECM1 p.Arg53Ter Pathogenic ★★ same condition
- ECM1 p.Cys269Tyr Pathogenic/Likely pathogenic ★★ same condition
- ECM1 p.Pro78fs Pathogenic/Likely pathogenic ★★ same condition
- ECM1 c.122-3T>G Uncertain significance ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ecm1-p-cys181ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown