EXPH5 p.Ser873=
c.2619G>A · rs114840330 · VCV740842
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.101%, afr)
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 -2.6 | GERP -3.7 |
| Overall | ||
| CADD | 3.943 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.101%
African / African-American · 76/75,044 alleles
Filtering AF
0.0829%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0762%
Overall
0.00774%
125/1,613,964 alleles · rare
exomes 83/1,461,664 · genomes 42/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.101% | 987 |
| Admixed American | 0.035% | 2,858 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,944 |
| East Asian | 0.00891% | 11,220 |
| Finnishnot grpmax-eligible | 0.00469% | 21,338 |
| European (non-Finnish) | 0.000932% | 107,266 |
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.Ser873=
- Coding
- c.2619G>A
- MANE Select
- NM_015065
- dbSNP
- rs114840330
- Type
- single nucleotide variant
- Location
- chr11:108512888 (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.Ser873Leu Likely benign ★ same residue
- 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
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-ser873 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown