MAP4 p.Asn569=
c.1707T>C · rs753451007 · VCV3033770
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, nfe)
Conditions
1
MAP4-related disorder
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 -0.17 | GERP -3.5 |
| Overall | ||
| CADD | 3.043 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
European (non-Finnish) · 126/1,180,044 alleles
Filtering AF
0.00911%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00855%
Overall
0.00805%
130/1,614,042 alleles · ultra-rare
exomes 127/1,461,892 · genomes 3/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0107% | 9,365 |
| African / African-American | 0.004% | 24,970 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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
- Protein
- p.Asn569=
- Coding
- c.1707T>C
- MANE Select
- NM_001385682
- dbSNP
- rs753451007
- Type
- single nucleotide variant
- Location
- chr3:47916120 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 43.03
Disease context
MAP4-related disorder
Similar variants
- MAP4 c.292+2409G>A Likely benign same condition
- MAP4 c.*100G>A Likely benign same condition
- MAP4 c.*44G>A Likely benign same condition
- MAP4 p.Ala2123= Likely benign same condition
- MAP4 p.Ala2134= Likely benign same condition
- MAP4 p.Ala437= Likely benign same condition
- MAP4 p.Arg23Gln Benign same condition
- MAP4 p.Arg23Trp Likely benign ⚠ same condition
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-p-asn569 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown