HOMER2 p.Val197=
c.591G>A · rs781482695 · VCV2971282
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0263%, sas)
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 -1.3 | GERP -2.3 |
| Overall | ||
| CADD | 7.625 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0263%
South Asian · 24/91,084 alleles
Filtering AF
0.0181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0154%
Overall
0.00353%
57/1,613,014 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0263% | 3,795 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,223 |
| European (non-Finnish) | 0.00254% | 39,330 |
| African / African-American | 0.00133% | 74,928 |
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
- HOMER2
- Protein
- p.Val197=
- Coding
- c.591G>A
- MANE Select
- NM_004839
- dbSNP
- rs781482695
- Type
- single nucleotide variant
- Location
- chr15:82854704 (GRCh38)
- Gene constraint
- LOEUF 0.921 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 89.20
Similar variants
- CPD p.Phe197Leu Likely benign ★ same residue
- HOMER2 p.Arg208Cys Uncertain significance ★★ ⚠ same type
- HOMER2 p.Arg213Trp Uncertain significance ★★ ⚠ same type
- HOMER2 p.Arg215His Uncertain significance ★★ ⚠ same type
- HOMER2 p.Arg309Cys Uncertain significance ★★ ⚠ same type
- HOMER2 p.Arg334Gln Uncertain significance ★★ ⚠ same type
- HOMER2 p.Asn235Lys Uncertain significance ★★ ⚠ same type
- HOMER2 p.Glu255Asp 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/homer2-p-val197 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown