ANGPT2 p.Ser164=
c.492C>T · rs144373407 · VCV735359
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.587%, 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 -0.14 | GERP -4, phastCons 0.05 |
| Overall | ||
| CADD | 0.324 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.587%
African / African-American · 440/75,008 alleles
Filtering AF
0.541%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.523%
Overall
0.0299%
483/1,613,844 alleles · rare
exomes 233/1,461,626 · genomes 250/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.587% | 170 |
| Admixed American | 0.0383% | 2,609 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,289 |
| European (non-Finnish) | 8.48e-05% | 1,179,884 |
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
- ANGPT2
- Protein
- p.Ser164=
- Coding
- c.492C>T
- MANE Select
- NM_001118887
- dbSNP
- rs144373407
- Type
- single nucleotide variant
- Location
- chr8:6527629 (GRCh38)
- Gene constraint
- LOEUF 0.606 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 84.15 · 7 PDB
Similar variants
- ANGPT2 p.Ile227Thr Uncertain significance ★★ ⚠ same type
- MCPH1 p.Leu730Gln Uncertain significance ★★ same type
- ANGPT2 c.566+9A>C Benign ★★ same type
- ANGPT2 p.Ala310Val Benign ★★ same type
- ANGPT2 p.Asp269His Benign/Likely benign ★★ same type
- ANGPT2 p.Leu402= Benign ★★ same type
- ANGPT2 p.Lys32= Benign ★★ same type
- ANGPT2 p.Thr154= 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/angpt2-p-ser164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown