UNC79 p.Phe1901Ser
c.5702T>C · rs774688629 · VCV1327054
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0121%, sas)
Conditions
1
autism spectrum disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.506 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 26.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0121%
South Asian · 11/91,080 alleles
Filtering AF
0.00676%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00522%
Overall
0.000682%
11/1,613,988 alleles · ultra-rare
exomes 10/1,461,868 · genomes 1/152,120 · joint denominator
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
- UNC79
- Protein
- p.Phe1901Ser
- Coding
- c.5702T>C
- MANE Select
- NM_001395159
- dbSNP
- rs774688629
- Type
- single nucleotide variant
- Location
- chr14:93622719 (GRCh38)
- Gene constraint
- LOEUF 0.168 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.95 · 3 PDB
- Residue 1901
- the 'disordered' region
Similar variants
- UNC79 p.Ile1680Thr Uncertain significance ★★ same type
- UNC79 p.Pro2467Arg Uncertain significance ★★ same type
- UNC79 p.Ser1741Cys Uncertain significance ★★ same type
- UNC79 p.Ser706Arg Uncertain significance ★★ same type
- UNC79 p.Thr2409Met Uncertain significance ★★ same type
- UNC79 p.Tyr539Phe Uncertain significance ★★ same type
- UNC79 c.3191-2A>C Likely pathogenic ★ same type
- UNC79 c.6134-1G>A Likely pathogenic ★ 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/unc79-p-phe1901ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown