ERBIN p.Ser1078=
c.3234T>C · rs760184576 · VCV1915517
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, 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 0.3 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 5.492 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
South Asian · 20/91,084 alleles
Filtering AF
0.0145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.00248%
40/1,613,960 alleles · ultra-rare
exomes 38/1,461,884 · genomes 2/152,076 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.022% | 4,554 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,623 |
| European (non-Finnish) | 0.00136% | 73,750 |
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
- ERBIN
- Protein
- p.Ser1078=
- Coding
- c.3234T>C
- MANE Select
- NM_001253697
- dbSNP
- rs760184576
- Type
- single nucleotide variant
- Location
- chr5:66054552 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 56.01 · 11 PDB
- Residue 1078
- the 'disordered' region
Similar variants
- ERBIN p.Ala942Val Uncertain significance ★★ ⚠ same type
- ERBIN p.Arg1096Gln Uncertain significance ★★ ⚠ same type
- ERBIN p.Arg1166Gln Uncertain significance ★★ ⚠ same type
- ERBIN p.Asn1035Ser Uncertain significance ★★ ⚠ same type
- ERBIN p.Asn650Ser Uncertain significance ★★ ⚠ same type
- ERBIN p.Asp530Tyr Uncertain significance ★★ ⚠ same type
- ERBIN p.Cys658Ser Uncertain significance ★★ ⚠ same type
- ERBIN p.His521Arg 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/erbin-p-ser1078 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown