Is CCL20 p.Arg87His (c.260G>A) pathogenic?

CCL20 p.Arg87His (c.260G>A) is classified Likely benign in CCL20 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-05). AlphaMissense: likely benign (0.0824); Ultra-rare (popmax 0.0121%, afr).

How common is CCL20 p.Arg87His (c.260G>A) in the general population?

CCL20 p.Arg87His (c.260G>A) is ultra-rare (popmax 0.0121%, afr) (gnomAD).

What do computational predictors say about CCL20 p.Arg87His (c.260G>A)?

AlphaMissense predicts likely benign (score 0.0824) — an in-silico prediction, not a clinical call.

CCL20 p.Arg87His

c.260G>A · rs765540742 · VCV3139723

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0824 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0121%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0824	likely benign
REVEL	0.011	strongly benign-leaning
SaProt	LLR -7.48	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 -2.1	GERP -4
Regional constraint	o/e 0.91	unconstrained · MANE · 3,168 bp · p 0.32 · regional, not allelic
Overall
CADD	0.415	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 0.0121% African / African-American · 9/74,422 alleles

Filtering AF 0.00627% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0047%

Overall 0.000881% 14/1,588,346 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0121%	8,269
East Asian	0.00224%	44,718
South Asian	0.00111%	90,438
European (non-Finnish)	0.000259%	385,676

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: CCL20
Protein: p.Arg87His
Coding: c.260G>A
MANE Select: NM_004591
dbSNP: rs765540742
Type: single nucleotide variant
Location: chr2:227816375 (GRCh38)
Gene constraint: LOEUF 1.849 · pLI 0.33 (gnomAD)
Structure: AlphaFold pLDDT 89.36 · 6 PDB
Residue 87: an α-helix

Full CCL20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCL20 p.Arg87Cys Uncertain significance ★ ⚠ same residue
CCL20 p.Asn61Ser Uncertain significance ★ ⚠ same type
CCL20 p.Gly57Val Uncertain significance ★ ⚠ same type
CCL20 p.Ile64Val Uncertain significance ★ ⚠ same type
CCL20 p.Leu9Pro Uncertain significance ★ ⚠ same type
CCL20 p.Ser14Leu Uncertain significance ★ ⚠ same type
CCL20 p.Arg39His Likely benign ★ ⚠ same type
CCL20 p.Arg51Gln Likely benign ★ 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/ccl20-p-arg87his (accessed [today's date]).

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