Is CCR1 p.Ser340Ile (c.1019G>T) pathogenic?

CCR1 p.Ser340Ile (c.1019G>T) is classified Uncertain significance in CCR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-10). AlphaMissense: likely benign (0.171); Very rare (popmax 0.00415%, nfe).

How common is CCR1 p.Ser340Ile (c.1019G>T) in the general population?

CCR1 p.Ser340Ile (c.1019G>T) is very rare (popmax 0.00415%, nfe) (gnomAD).

What do computational predictors say about CCR1 p.Ser340Ile (c.1019G>T)?

AlphaMissense predicts likely benign (score 0.171) — an in-silico prediction, not a clinical call.

CCR1 p.Ser340Ile

c.1019G>T · rs61755290 · VCV2474860

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.171 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00415%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.171	likely benign
REVEL	0.358	indeterminate
SaProt	LLR -9.35	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.8	GERP 1.4, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 1,064 bp · p 3.5e-05 · regional, not allelic
Overall
CADD	22.6	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 0.00415% European (non-Finnish) · 49/1,180,020 alleles

Filtering AF 0.00318% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00286%

Overall 0.00316% 51/1,614,048 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00415%	24,082
Admixed American	0.00333%	29,999

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: CCR1
Protein: p.Ser340Ile
Coding: c.1019G>T
MANE Select: NM_001295
dbSNP: rs61755290
Type: single nucleotide variant
Location: chr3:46203295 (GRCh38)
Gene constraint: LOEUF 1.931 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 83.49 · 3 PDB

Full CCR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCR1 p.Ala159Val Likely benign ★★ same type
CCR1 p.Leu127= Benign ★★ same type
CCR1 p.Leu54= Benign/Likely benign ★★ same type
CCR1 p.Ter356= Benign ★★ same type
CCR1 p.Thr146= Likely benign ★★ same type
CCR1 p.Tyr291His Benign ★★ same type
CCR1 p.Tyr301= Benign/Likely benign ★★ same type
CCR1 p.Ala159Ser 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/ccr1-p-ser340ile (accessed [today's date]).

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