DDHD2 p.Arg297=
c.891G>A · rs369986054 · VCV2658543
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.07 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.77 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 7.884 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,024 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,461,840 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
- DDHD2
- Protein
- p.Arg297=
- Coding
- c.891G>A
- MANE Select
- NM_015214
- dbSNP
- rs369986054
- Type
- single nucleotide variant
- Location
- chr8:38245784 (GRCh38)
- Gene constraint
- LOEUF 0.758 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.70
- Residue 297
- a UniProt-annotated variant site (in spg54; likely pathogenic; loss of triacylglycerol hydrolase activity)
Similar variants
- DDHD2 c.1126-2A>G Likely pathogenic ★★ same type
- DDHD2 c.1248+2T>C Likely pathogenic ★★ same type
- DDHD2 p.Arg232Ter Pathogenic ★★ same type
- DDHD2 p.Arg329Ter Pathogenic ★★ same type
- DDHD2 p.Arg422Ter Likely pathogenic ★★ same type
- DDHD2 p.Arg516Ter Pathogenic ★★ same type
- DDHD2 p.Asp660His Pathogenic/Likely pathogenic ★★ same type
- DDHD2 p.Gln286Ter 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/ddhd2-p-arg297 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown