CLN6 p.Phe238=
c.714C>T · rs772090270 · VCV1657298
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00892%, eas)
Conditions
1
neuronal ceroid lipofuscinosis
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 6.2 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 13.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,858 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000274%
4/1,461,584 alleles · very rare
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
- CLN6
- Protein
- p.Phe238=
- Coding
- c.714C>T
- MANE Select
- NM_017882
- dbSNP
- rs772090270
- Type
- single nucleotide variant
- Location
- chr15:68208362 (GRCh38)
- Gene constraint
- LOEUF 1.015 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.86
- Residue 238
- a UniProt-annotated variant site (in cln4a; requires 2 nucleotide substitutions)
Similar variants
- CLN6 p.Phe238Thr Pathogenic/Likely pathogenic ★★ same residue
- CLN6 c.297+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CLN6 c.486+1G>A Likely pathogenic ★★ same condition
- CLN6 c.543-1G>A Likely pathogenic ★★ same condition
- CLN6 c.665+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CLN6 c.84-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CLN6 p.Arg103Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CLN6 p.Arg149Cys Likely pathogenic ★★ same condition
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/cln6-p-phe238 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown