CALD1 p.Ser665=
c.1995G>A · rs61755270 · VCV742033
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0344%, 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 0.81 | GERP 0.65, phastCons 0.038 |
| Overall | ||
| CADD | 7.669 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0344%
European (non-Finnish) · 406/1,179,956 alleles
Filtering AF
0.0316%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0306%
Overall
0.0268%
433/1,613,732 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0344% | 2,906 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,676 |
| Middle Eastern | 0.0165% | 6,062 |
| Finnishnot grpmax-eligible | 0.00782% | 12,787 |
| Admixed American | 0.00334% | 29,980 |
| African / African-American | 0.00267% | 37,441 |
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
- CALD1
- Protein
- p.Ser665=
- Coding
- c.1995G>A
- MANE Select
- NM_033138
- dbSNP
- rs61755270
- Type
- single nucleotide variant
- Location
- chr7:134958224 (GRCh38)
- Gene constraint
- LOEUF 0.498 · pLI 0.96 (gnomAD)
- Structure
- AlphaFold pLDDT 65.68
- Residue 665
- the 'strong actin-binding' region; the 'tropomyosin-binding' region
Similar variants
- CALD1 p.Ser665Leu Uncertain significance ★ ⚠ same residue
- CALD1 p.Ala324Glu Benign ★★ ⚠ same type
- CALD1 p.Asp122Asn Likely benign ★★ same type
- CALD1 p.Glu77Lys Benign ★★ same type
- CALD1 p.Ile671Val Benign ★★ same type
- CALD1 p.Met257Ile Likely benign ★★ same type
- CALD1 p.Ser171Phe Benign ★★ same type
- CALD1 p.Ala265Thr 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/cald1-p-ser665 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown