CTCFL p.Ala238=
c.714T>C · rs750244176 · VCV2652426
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, 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 -3.2 | GERP -4.4 |
| Overall | ||
| CADD | 0.417 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,904 alleles
Filtering AF
0.000688%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00093%
15/1,613,770 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,904 |
| European (non-Finnish) | 0.00119% | 84,284 |
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
- CTCFL
- Protein
- p.Ala238=
- Coding
- c.714T>C
- MANE Select
- NM_001386993
- dbSNP
- rs750244176
- Type
- single nucleotide variant
- Location
- chr20:57523108 (GRCh38)
- Gene constraint
- LOEUF 0.669 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.75
- Residue 238
- the 'disordered' region
Similar variants
- CTCFL p.Ser172= Benign ★★ same type
- CTCFL p.Val652Met Benign ★★ same type
- CTCFL p.Ala155Ser Uncertain significance ★ ⚠ same type
- CTCFL p.Ala155Thr Uncertain significance ★ ⚠ same type
- CTCFL p.Ala253Thr Uncertain significance ★ ⚠ same type
- CTCFL p.Ala321Thr Uncertain significance ★ ⚠ same type
- CTCFL p.Ala434Thr Uncertain significance ★ ⚠ same type
- CTCFL p.Ala438Thr Uncertain significance ★ ⚠ 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/ctcfl-p-ala238 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown