UTRN p.Phe1440=
c.4320C>T · VCV4198195
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0245%, eas)
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 -5.1 | GERP -3.7 |
| Overall | ||
| CADD | 7.894 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0245%
East Asian · 11/44,856 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00167%
27/1,612,258 alleles · ultra-rare
exomes 24/1,459,928 · genomes 3/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0245% | 4,078 |
| Middle Eastern | 0.0165% | 6,058 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,809 |
| South Asian | 0.0011% | 90,750 |
| European (non-Finnish) | 0.000933% | 107,189 |
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
- UTRN
- Protein
- p.Phe1440=
- Coding
- c.4320C>T
- MANE Select
- NM_007124
- Type
- single nucleotide variant
- Location
- chr6:144490985 (GRCh38)
- Gene constraint
- LOEUF 0.665 · pLI <0.01 (gnomAD)
- Residue 1440
- the 'interaction with synm' region
Similar variants
- UTRN c.4437+9T>C Benign/Likely benign ★★ same type
- UTRN c.4594-8C>T Benign/Likely benign ★★ same type
- UTRN p.Arg1625Lys Likely benign ★★ same type
- UTRN p.Arg1967Trp Benign/Likely benign ★★ same type
- UTRN p.Gly1862Glu Likely benign ★★ same type
- UTRN p.Ile2227Val Likely benign ★★ same type
- UTRN p.Ser1561Cys Likely benign ★★ same type
- UTRN p.Thr2288= Likely benign ★★ 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/utrn-p-phe1440 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown