Is CCR2 p.Val52= (c.156G>T) pathogenic?

CCR2 p.Val52= (c.156G>T) is classified Benign in CCR2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-07-31). Rare (popmax 0.993%, nfe).

How common is CCR2 p.Val52= (c.156G>T) in the general population?

CCR2 p.Val52= (c.156G>T) is rare (popmax 0.993%, nfe) (gnomAD).

CCR2 p.Val52=

c.156G>T · rs3918367 · VCV714233

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.993%, nfe)

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 2.8	phastCons 1
Overall
CADD	5.692	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.993% European (non-Finnish) · 11,714/1,180,018 alleles

Filtering AF 0.978% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.971%

Overall 0.884% 14,264/1,614,122 alleles · rare exomes 13,203/1,461,876 · genomes 1,061/152,246 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.69%	59
European (non-Finnish)grpmax	0.993%	101
South Asian	0.769%	130
Remaining individualsnot grpmax-eligible	0.686%	146
Middle Eastern	0.412%	242
Admixed American	0.277%	362
African / African-American	0.157%	636
Ashkenazi Jewishnot grpmax-eligible	0.0946%	1,057
East Asian	0.0111%	8,976

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CCR2
Protein: p.Val52=
Coding: c.156G>T
MANE Select: NM_001123396
dbSNP: rs3918367
Type: single nucleotide variant
Location: chr3:46357683 (GRCh38)
Gene constraint: LOEUF 1.825 · pLI 0.05 (gnomAD)
Structure: AlphaFold pLDDT 78.28 · 7 PDB
Residue 52: an α-helix

Full CCR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCR2 c.*1179G>A Uncertain significance ★★ ⚠ same type
CCR2 p.Arg196Ter Likely pathogenic ★ same type
CCR2 c.*1068C>A Uncertain significance ★ ⚠ same type
CCR2 c.*1141C>A Uncertain significance ★ ⚠ same type
CCR2 c.*1168A>G Uncertain significance ★ ⚠ same type
CCR2 c.*1176C>G Uncertain significance ★ ⚠ same type
CCR2 c.*1198A>G Uncertain significance ★ ⚠ same type
CCR2 c.*1218G>A 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/ccr2-p-val52 (accessed [today's date]).

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