LAMC3 p.Ser853=
c.2559C>T · rs34652877 · VCV129457
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.06%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.7 | GERP -4 |
| Overall | ||
| CADD | 2.126 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.06%
European (non-Finnish) · 36,166/1,180,002 alleles
Filtering AF
3.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.03%
Overall
2.63%
42,446/1,614,058 alleles · low-frequency
exomes 39,549/1,461,792 · genomes 2,897/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 3.06% | 33 |
| Middle Eastern | 2.89% | 35 |
| Remaining individualsnot grpmax-eligible | 2.43% | 41 |
| Ashkenazi Jewishnot grpmax-eligible | 2.14% | 47 |
| Admixed American | 1.8% | 56 |
| Finnishnot grpmax-eligible | 1.7% | 59 |
| South Asian | 1.55% | 64 |
| African / African-American | 0.482% | 207 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| East Asian | 0.0156% | 6,411 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- LAMC3
- Protein
- p.Ser853=
- Coding
- c.2559C>T
- MANE Select
- NM_006059
- dbSNP
- rs34652877
- Type
- single nucleotide variant
- Location
- chr9:131067171 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.23
- Residue 853
- the laminin egf-like 8 domain
Similar variants
- LAMC3 c.1166-1G>A Likely pathogenic ★★ same type
- LAMC3 c.3211+1G>A Likely pathogenic ★★ same type
- LAMC3 c.3211+2T>C Likely pathogenic ★★ same type
- LAMC3 c.976+1G>A Pathogenic ★★ same type
- LAMC3 p.Cys810Ter Pathogenic ★★ same type
- LAMC3 p.Gln550Ter Pathogenic ★★ same type
- LAMC3 p.Ser421Ter Pathogenic ★★ same type
- LAMC3 p.Ala1090Ser Uncertain significance ★★ ⚠ same type
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/lamc3-p-ser853 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown