DLEC1 p.Ser1268=
c.3804C>T · rs116619354 · VCV786005
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.25%, afr) — too common for a highly-penetrant pathogenic allele
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 -2.2 | GERP -3.9 |
| Overall | ||
| CADD | 8.232 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.25%
African / African-American · 4,688/75,042 alleles
Filtering AF
6.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.04%
Overall
0.338%
5,448/1,613,836 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.25% | 16 |
| Admixed American | 0.44% | 227 |
| Remaining individualsnot grpmax-eligible | 0.421% | 238 |
| Middle Eastern | 0.379% | 264 |
| Ashkenazi Jewishnot grpmax-eligible | 0.27% | 370 |
| South Asian | 0.0176% | 5,685 |
| European (non-Finnish) | 0.00932% | 10,726 |
| East Asian | 0.00891% | 11,220 |
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
- DLEC1
- Protein
- p.Ser1268=
- Coding
- c.3804C>T
- MANE Select
- NM_007335
- dbSNP
- rs116619354
- Type
- single nucleotide variant
- Location
- chr3:38115001 (GRCh38)
- Gene constraint
- LOEUF 0.813 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.51
Similar variants
- DLEC1 p.Ala727= Benign ★★ same type
- DLEC1 p.Asn885= Benign ★★ same type
- DLEC1 p.Leu1219= Likely benign ★★ same type
- DLEC1 p.Leu1672= Benign ★★ same type
- DLEC1 p.Leu871= Benign/Likely benign ★★ same type
- DLEC1 p.Lys1022Asn Benign ★★ same type
- DLEC1 p.Ser181= Benign ★★ same type
- DLEC1 p.Ser192Phe Benign ★★ 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/dlec1-p-ser1268 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown