Is ERBIN p.Ala628Val (c.1883C>T) pathogenic?

ERBIN p.Ala628Val (c.1883C>T) is classified Uncertain significance in ERBIN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-27). AlphaMissense: likely benign (0.1973); Ultra-rare (popmax 0.0256%, afr).

How common is ERBIN p.Ala628Val (c.1883C>T) in the general population?

ERBIN p.Ala628Val (c.1883C>T) is ultra-rare (popmax 0.0256%, afr) (gnomAD).

What do computational predictors say about ERBIN p.Ala628Val (c.1883C>T)?

AlphaMissense predicts likely benign (score 0.1973) — an in-silico prediction, not a clinical call.

ERBIN p.Ala628Val

c.1883C>T · rs142201440 · VCV1380078

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1973 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0256%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1973	likely benign
REVEL	0.169	moderately benign-leaning
SaProt	LLR -4.95	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 5, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 30 kb · p 0.011 · regional, not allelic
Overall
CADD	26.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0256% African / African-American · 19/74,160 alleles

Filtering AF 0.0167% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0139%

Overall 0.00125% 20/1,595,956 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0256%	3,903
Remaining individualsnot grpmax-eligible	0.00162%	61,728

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.Ala628Val
Coding: c.1883C>T
MANE Select: NM_001253697
dbSNP: rs142201440
Type: single nucleotide variant
Location: chr5:66048761 (GRCh38)
Gene constraint: LOEUF 0.526 · pLI 0.72 (gnomAD)
Structure: AlphaFold pLDDT 56.01 · 11 PDB
Residue 628: the 'disordered' region

Full ERBIN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ERBIN p.Ala628= Likely benign ★ same residue
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

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-ala628val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown