LAMB3 p.Ser875=
c.2625C>T · rs768028663 · VCV1147908
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00934%, afr)
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 2.1 | GERP -0.29, phastCons 0.99 |
| Overall | ||
| CADD | 11.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00934%
African / African-American · 7/74,908 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.0013%
21/1,613,992 alleles · very rare
exomes 16/1,461,846 · genomes 5/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00934% | 10,701 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 0.0011% | 90,770 |
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
- LAMB3
- Protein
- p.Ser875=
- Coding
- c.2625C>T
- MANE Select
- NM_000228
- dbSNP
- rs768028663
- Type
- single nucleotide variant
- Location
- chr1:209622612 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.55
- Residue 875
- the 'domain i' region
Similar variants
- LAMB3 c.1132+5G>A Pathogenic/Likely pathogenic ★★ same type
- LAMB3 c.1133-22G>A Pathogenic ★★ same type
- LAMB3 c.1288+1G>T Pathogenic/Likely pathogenic ★★ same type
- LAMB3 c.1486-1G>A Likely pathogenic ★★ same type
- LAMB3 c.1597+1G>T Likely pathogenic ★★ same type
- LAMB3 c.2138-1G>A Likely pathogenic ★★ same type
- LAMB3 c.2701+2T>C Likely pathogenic ★★ same type
- LAMB3 c.28+1G>T Likely pathogenic ★★ 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/lamb3-p-ser875 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown