MAP4 c.*69G>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.05%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.096 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP 1.8, phastCons 1 |
| Non-coding constraint | Z 3.40 | 1 kb window · o/e 0.71 · regional · uncalibrated |
| Overall | ||
| CADD | 19.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.05%
Middle Eastern · 3/5,998 alleles
Filtering AF
0.0316%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0305%
Overall
0.0284%
445/1,569,108 alleles · ultra-rare
exomes 412/1,416,826 · genomes 33/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.05% | 1,999 |
| Remaining individualsnot grpmax-eligible | 0.0361% | 2,767 |
| European (non-Finnish) | 0.0344% | 2,907 |
| Admixed American | 0.0172% | 5,807 |
| South Asian | 0.00578% | 17,296 |
| African / African-American | 0.00543% | 18,428 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00348% | 28,776 |
| Finnishnot grpmax-eligible | 0.00328% | 30,518 |
| East Asian | 0.00239% | 41,896 |
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
- MAP4
- Coding
- c.*69G>A
- MANE Select
- NM_001385682
- dbSNP
- rs780981104
- Type
- single nucleotide variant
- Location
- chr3:47852865 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 43.03
Similar variants
- MAP4 c.292+9T>G Benign ★★ same type
- MAP4 p.Gln1950= Benign ★★ same type
- MAP4 p.Leu516= Likely benign ★★ same type
- MAP4 p.Val37= Benign ★★ same type
- MAP4 p.Ala150Ser Uncertain significance ★ ⚠ same type
- MAP4 p.Ala1922Val Uncertain significance ★ ⚠ same type
- MAP4 p.Ala1926Pro Uncertain significance ★ ⚠ same type
- MAP4 p.Ala1941Thr 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/map4-c-star-69g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown