PDE6A p.Leu72=
c.216A>G · rs570928102 · VCV1576650
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.186%, sas)
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 -0.37 | GERP -5.5, phastCons 0.15 |
| Overall | ||
| CADD | 5.183 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.186%
South Asian · 169/91,076 alleles
Filtering AF
0.163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.154%
Overall
0.0107%
173/1,614,178 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.186% | 539 |
| Middle Eastern | 0.0165% | 6,058 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,836 |
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
- PDE6A
- Protein
- p.Leu72=
- Coding
- c.216A>G
- MANE Select
- NM_000440
- dbSNP
- rs570928102
- Type
- single nucleotide variant
- Location
- chr5:149944458 (GRCh38)
- Gene constraint
- LOEUF 0.888 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.80
- Residue 72
- the gaf 1 domain
Similar variants
- PDE6A c.1065+2T>A Pathogenic/Likely pathogenic ★★ same type
- PDE6A c.1263+1G>T Pathogenic/Likely pathogenic ★★ same type
- PDE6A c.1407+1G>C Pathogenic/Likely pathogenic ★★ same type
- PDE6A c.1620+1G>A Pathogenic ★★ same type
- PDE6A c.1620+2T>A Pathogenic/Likely pathogenic ★★ same type
- PDE6A c.1926+1G>A Pathogenic ★★ same type
- PDE6A c.1927-1G>C Pathogenic/Likely pathogenic ★★ same type
- PDE6A c.2027+2T>G Pathogenic/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/pde6a-p-leu72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown