Is CCL23 p.Pro54Ser (c.160C>T) pathogenic?

CCL23 p.Pro54Ser (c.160C>T) is classified Uncertain significance in CCL23 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-17). Absent from gnomAD v4.1.

How common is CCL23 p.Pro54Ser (c.160C>T) in the general population?

CCL23 p.Pro54Ser (c.160C>T) is absent from gnomAD v4.1 (gnomAD).

CCL23 p.Pro54Ser

c.160C>T · VCV3997495

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.026	moderately benign-leaning
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.22 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.1	phastCons 0.006
Overall
CADD	1.952	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CCL23
Protein: p.Pro54Ser
Coding: c.160C>T
MANE Select: NM_005064
Type: single nucleotide variant
Location: chr17:36013886 (GRCh38)
Gene constraint: LOEUF 1.412 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.75 · 1 PDB
Residue 54: a disulfide bond

Full CCL23 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCL23 p.Ala66Val Uncertain significance ★ ⚠ same type
CCL23 p.Ala6Thr Uncertain significance ★ ⚠ same type
CCL23 p.Arg108Pro Uncertain significance ★ ⚠ same type
CCL23 p.Arg131Gln Uncertain significance ★ ⚠ same type
CCL23 p.Arg78Gln Uncertain significance ★ ⚠ same type
CCL23 p.Asp70Asn Uncertain significance ★ ⚠ same type
CCL23 p.Gln118Lys Uncertain significance ★ ⚠ same type
CCL23 p.Glu30Lys 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/ccl23-p-pro54ser (accessed [today's date]).

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