Is COG1 p.Arg383Gln (c.1148G>A) pathogenic?

COG1 p.Arg383Gln (c.1148G>A) is classified Uncertain significance in COG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-02). AlphaMissense: ambiguous (0.4907); Ultra-rare (popmax 0.0165%, mid); Associated with Inborn genetic diseases.

What condition is associated with COG1 p.Arg383Gln (c.1148G>A)?

COG1 p.Arg383Gln (c.1148G>A) is associated with Inborn genetic diseases (ClinVar).

How common is COG1 p.Arg383Gln (c.1148G>A) in the general population?

COG1 p.Arg383Gln (c.1148G>A) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about COG1 p.Arg383Gln (c.1148G>A)?

AlphaMissense predicts ambiguous (score 0.4907) — an in-silico prediction, not a clinical call.

COG1 p.Arg383Gln

c.1148G>A · rs149528257 · VCV3147067

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4907 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4907	ambiguous
REVEL	0.515	indeterminate
SaProt	LLR -12.56	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.5, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 15 kb · p 0.052 · regional, not allelic
Overall
CADD	27.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,078 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00162%

Overall 0.00149% 24/1,614,012 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,078
African / African-American	0.00668%	14,979
South Asian	0.00439%	22,770
Remaining individualsnot grpmax-eligible	0.0032%	31,242
East Asian	0.00223%	44,890
Admixed American	0.00167%	59,982
European (non-Finnish)	0.000847%	118,005

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: COG1
Protein: p.Arg383Gln
Coding: c.1148G>A
MANE Select: NM_018714
dbSNP: rs149528257
Type: single nucleotide variant
Location: chr17:73200643 (GRCh38)
Gene constraint: LOEUF 0.718 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 77.82

Full COG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COG1 p.Arg383= Likely benign ★ same residue
COG1 p.Ala209Val Uncertain significance ★★ ⚠ same condition
COG1 p.Ala27Ser Uncertain significance ★★ ⚠ same condition
COG1 p.Ala380Val Uncertain significance ★★ ⚠ same condition
COG1 p.Ala385Thr Uncertain significance ★★ ⚠ same condition
COG1 p.Ala563Val Uncertain significance ★★ ⚠ same condition
COG1 p.Arg165Gln Uncertain significance ★★ ⚠ same condition
COG1 p.Arg172Trp Uncertain significance ★★ ⚠ same condition

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/cog1-p-arg383gln (accessed [today's date]).

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