Is CCR1 p.Ter356= (c.1067G>A) pathogenic?

CCR1 p.Ter356= (c.1067G>A) is classified Benign in CCR1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-07-29). Low-frequency (popmax 3.45%, afr).

How common is CCR1 p.Ter356= (c.1067G>A) in the general population?

CCR1 p.Ter356= (c.1067G>A) is low-frequency (popmax 3.45%, afr) (gnomAD).

CCR1 p.Ter356=

c.1067G>A · rs41413045 · VCV775865

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

stop-loss

predicted LoF

gnomAD v4.1

Rare

low-frequency (popmax 3.45%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	stop-loss	predicted loss-of-function
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1	GERP 2.2, phastCons 1
Overall
CADD	13.23	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.45% African / African-American · 2,582/74,938 alleles

Filtering AF 3.33% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.29%

Overall 0.193% 3,104/1,610,120 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.45%	29
Remaining individualsnot grpmax-eligible	0.289%	346
Middle Eastern	0.215%	465
Admixed American	0.21%	475
European (non-Finnish)	0.0162%	6,164
South Asian	0.0121%	8,243
East Asian	0.00223%	44,788

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.Ter356=
Coding: c.1067G>A
MANE Select: NM_001295
dbSNP: rs41413045
Type: single nucleotide variant
Location: chr3:46203247 (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.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
CCR1 p.Ala200Val 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-ter356 (accessed [today's date]).

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