DIP2C p.Ser654=
c.1962G>A · rs142691003 · VCV734752
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.181%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.104 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7.5 | GERP -3.7 |
| Overall | ||
| CADD | 0.992 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.181%
Middle Eastern · 11/6,062 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0787%
Overall
0.0535%
863/1,613,802 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.181% | 551 |
| European (non-Finnish) | 0.0639% | 1,565 |
| Admixed American | 0.0417% | 2,400 |
| South Asian | 0.0363% | 2,756 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,976 |
| African / African-American | 0.0173% | 5,771 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,794 |
| East Asian | 0.00668% | 14,962 |
| Finnishnot grpmax-eligible | 0.00156% | 63,994 |
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
- DIP2C
- Protein
- p.Ser654=
- Coding
- c.1962G>A
- MANE Select
- NM_014974
- dbSNP
- rs142691003
- Type
- single nucleotide variant
- Location
- chr10:382676 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.64
Similar variants
- DIP2C p.Ser654Leu Uncertain significance ★ ⚠ same residue
- DIP2C p.Ala1066Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1066Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1101Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1155Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1466Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala193Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala422Thr 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/dip2c-p-ser654 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown