GGCT p.Pro153=
c.459G>A · rs115910467 · VCV711870
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.954%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.153 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.7 | GERP -3.5 |
| Overall | ||
| CADD | 2.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.954%
African / African-American · 713/74,770 alleles
Filtering AF
0.896%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.872%
Overall
0.0796%
1,283/1,610,802 alleles · rare
exomes 817/1,458,574 · genomes 466/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.954% | 105 |
| Middle Eastern | 0.182% | 550 |
| Admixed American | 0.141% | 710 |
| Remaining individualsnot grpmax-eligible | 0.106% | 944 |
| South Asian | 0.0376% | 2,663 |
| European (non-Finnish) | 0.03% | 3,338 |
| Finnishnot grpmax-eligible | 0.0266% | 3,758 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,389 |
| East Asian | 0.00223% | 44,774 |
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
- GGCT
- Protein
- p.Pro153=
- Coding
- c.459G>A
- MANE Select
- NM_024051
- dbSNP
- rs115910467
- Type
- single nucleotide variant
- Location
- chr7:30497200 (GRCh38)
- Gene constraint
- LOEUF 1.335 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.67 · 5 PDB
Similar variants
- GGCT p.Asn35Ser Uncertain significance ★ ⚠ same type
- GGCT p.Asn90Tyr Uncertain significance ★ ⚠ same type
- GGCT p.Asp167Asn Uncertain significance ★ ⚠ same type
- GGCT p.Asp167Glu Uncertain significance ★ ⚠ same type
- GGCT p.Glu131Gly Uncertain significance ★ ⚠ same type
- GGCT p.Gly183Ala Uncertain significance ★ ⚠ same type
- GGCT p.Gly23Ser Uncertain significance ★ ⚠ same type
- GGCT p.Gly81Val 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/ggct-p-pro153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown