Is CCR1 p.Phe248Val (c.742T>G) pathogenic?

CCR1 p.Phe248Val (c.742T>G) is classified Uncertain significance in CCR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-12). AlphaMissense: likely pathogenic (0.6983); Absent from gnomAD v4.1.

How common is CCR1 p.Phe248Val (c.742T>G) in the general population?

CCR1 p.Phe248Val (c.742T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCR1 p.Phe248Val (c.742T>G)?

AlphaMissense predicts likely pathogenic (score 0.6983) — an in-silico prediction, not a clinical call.

CCR1 p.Phe248Val

c.742T>G · rs2529298183 · VCV2229767

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6983 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6983	likely pathogenic
REVEL	0.639	indeterminate
SaProt	LLR -12.85	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.3, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 1,064 bp · p 3.5e-05 · regional, not allelic
Overall
CADD	27.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

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: CCR1
Protein: p.Phe248Val
Coding: c.742T>G
MANE Select: NM_001295
dbSNP: rs2529298183
Type: single nucleotide variant
Location: chr3:46203572 (GRCh38)
Gene constraint: LOEUF 1.931 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 83.49 · 3 PDB
Residue 248: a disulfide bond; an α-helix

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-phe248val (accessed [today's date]).

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