Is C8B p.Arg520Cys (c.1558C>T) pathogenic?

C8B p.Arg520Cys (c.1558C>T) is classified Uncertain significance in C8B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-26). AlphaMissense: likely benign (0.1824); Ultra-rare (popmax 0.0106%, nfe); Associated with Inborn genetic diseases.

What condition is associated with C8B p.Arg520Cys (c.1558C>T)?

C8B p.Arg520Cys (c.1558C>T) is associated with Inborn genetic diseases (ClinVar).

How common is C8B p.Arg520Cys (c.1558C>T) in the general population?

C8B p.Arg520Cys (c.1558C>T) is ultra-rare (popmax 0.0106%, nfe) (gnomAD).

What do computational predictors say about C8B p.Arg520Cys (c.1558C>T)?

AlphaMissense predicts likely benign (score 0.1824) — an in-silico prediction, not a clinical call.

C8B p.Arg520Cys

c.1558C>T · rs778114966 · VCV1054845

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1824 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0106%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1824	likely benign
REVEL	0.194	benign-leaning
SaProt	LLR -10.50	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.2, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 37 kb · p 0.016 · regional, not allelic
Overall
CADD	27.7	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0106% European (non-Finnish) · 125/1,178,442 alleles

Filtering AF 0.00907% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00845%

Overall 0.0085% 137/1,611,388 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0106%	9,428
African / African-American	0.00668%	14,972
East Asian	0.00446%	22,429
Remaining individualsnot grpmax-eligible	0.00321%	31,184
Admixed American	0.00167%	59,948
Finnishnot grpmax-eligible	0.00158%	63,338
South Asian	0.0011%	91,032

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: C8B
Protein: p.Arg520Cys
Coding: c.1558C>T
MANE Select: NM_000066
dbSNP: rs778114966
Type: single nucleotide variant
Location: chr1:56931873 (GRCh38)
Gene constraint: LOEUF 1.18 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.99 · 8 PDB
Residue 520: the egf-like domain; a disulfide bond; a UniProt-annotated variant site (in c8d2); a β-strand

Full C8B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

C8B p.Arg520His Uncertain significance ★ ⚠ same residue
C8B p.Ala21Thr Uncertain significance ★★ ⚠ same condition
C8B p.Ala446Val Uncertain significance ★★ ⚠ same condition
C8B p.Arg136Cys Uncertain significance ★★ ⚠ same condition
C8B p.Arg136His Uncertain significance ★★ ⚠ same condition
C8B p.Arg156Gly Uncertain significance ★★ ⚠ same condition
C8B p.Arg296Cys Uncertain significance ★★ ⚠ same condition
C8B p.Arg296His Uncertain significance ★★ ⚠ same condition

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/c8b-p-arg520cys (accessed [today's date]).

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