DLEC1 p.Ser1498=
c.4494T>C · rs200734144 · VCV747796
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00559%, 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 -7.9 | GERP -3.2 |
| Overall | ||
| CADD | 3.128 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00559%
European (non-Finnish) · 66/1,179,946 alleles
Filtering AF
0.00451%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00411%
Overall
0.00421%
68/1,613,750 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00559% | 17,878 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,248 |
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.Ser1498=
- Coding
- c.4494T>C
- MANE Select
- NM_007335
- dbSNP
- rs200734144
- Type
- single nucleotide variant
- Location
- chr3:38117814 (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.Ser1268= Benign ★★ same type
- DLEC1 p.Ser181= 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-ser1498 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown