EXPH5 p.Ser393=
c.1179A>T · rs755374417 · VCV1539901
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0264%, sas)
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 -0.72 | GERP -2.2, phastCons 0.022 |
| Overall | ||
| CADD | 2.852 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0264%
South Asian · 24/90,894 alleles
Filtering AF
0.0181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0154%
Overall
0.00155%
25/1,613,260 alleles · ultra-rare
exomes 24/1,461,074 · genomes 1/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0264% | 3,787 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,466 |
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
- EXPH5
- Protein
- p.Ser393=
- Coding
- c.1179A>T
- MANE Select
- NM_015065
- dbSNP
- rs755374417
- Type
- single nucleotide variant
- Location
- chr11:108514328 (GRCh38)
- Gene constraint
- LOEUF 1.142 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 36.39
Similar variants
- EXPH5 p.Ala1429Ser Uncertain significance ★★ ⚠ same type
- EXPH5 p.Arg1727Lys Uncertain significance ★★ ⚠ same type
- EXPH5 p.Asn1548Asp Uncertain significance ★★ ⚠ same type
- EXPH5 p.Asp741His Uncertain significance ★★ ⚠ same type
- EXPH5 p.Gln1464Arg Uncertain significance ★★ ⚠ same type
- EXPH5 p.Gly54Arg Uncertain significance ★★ ⚠ same type
- EXPH5 p.Leu1519Arg Uncertain significance ★★ ⚠ same type
- EXPH5 p.Leu234Phe 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/exph5-p-ser393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown