EXPH5 p.Ser1868=
c.5604C>T · VCV4807482
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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -3.4 |
| Overall | ||
| CADD | 3.364 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.05%
Middle Eastern · 3/6,002 alleles
Filtering AF
0.0232%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.02%
Overall
0.0128%
206/1,606,486 alleles · ultra-rare
exomes 190/1,454,278 · genomes 16/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.05% | 2,001 |
| South Asian | 0.0324% | 3,082 |
| European (non-Finnish) | 0.014% | 7,135 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,533 |
| Admixed American | 0.00514% | 19,455 |
| African / African-American | 0.00268% | 37,283 |
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.Ser1868=
- Coding
- c.5604C>T
- MANE Select
- NM_015065
- Type
- single nucleotide variant
- Location
- chr11:108509903 (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-ser1868 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown