CD164L2 p.Val76=
c.228G>A · VCV3487841
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.052 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -0.38, phastCons 1 |
| Overall | ||
| CADD | 6.544 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,012 alleles
Filtering AF
0.00767%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00709%
Overall
0.00745%
120/1,611,500 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,012 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,906 |
| European (non-Finnish) | 0.00908% | 11,012 |
| Admixed American | 0.00668% | 14,961 |
| Finnishnot grpmax-eligible | 0.00156% | 63,926 |
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
- CD164L2
- Protein
- p.Val76=
- Coding
- c.228G>A
- MANE Select
- NM_001330448
- Type
- single nucleotide variant
- Location
- chr1:27382528 (GRCh38)
- Gene constraint
- LOEUF 1.268 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.70
- Residue 76
- a UniProt-annotated variant site (in)
Similar variants
- CD164L2 p.Ala132Thr Uncertain significance ★ ⚠ same type
- CD164L2 p.Ala24Thr Uncertain significance ★ same type
- CD164L2 p.Ala24Val Uncertain significance ★ ⚠ same type
- CD164L2 p.Ala40Ser Uncertain significance ★ ⚠ same type
- CD164L2 p.Ala53Thr Uncertain significance ★ ⚠ same type
- CD164L2 p.Arg104Leu Uncertain significance ★ ⚠ same type
- CD164L2 p.Arg10Pro Uncertain significance ★ ⚠ same type
- CD164L2 p.Arg43Pro 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/cd164l2-p-val76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown