Is CGN p.Thr1069Ala (c.3205A>G) pathogenic?

CGN p.Thr1069Ala (c.3205A>G) is classified Uncertain significance in CGN (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-10). Rare (popmax 0.149%, mid).

How common is CGN p.Thr1069Ala (c.3205A>G) in the general population?

CGN p.Thr1069Ala (c.3205A>G) is rare (popmax 0.149%, mid) (gnomAD).

CGN p.Thr1069Ala

c.3205A>G · rs77261959 · VCV2403708

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.149%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.12	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.8	GERP -0.92, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 3,161 bp · p 9.1e-06 · regional, not allelic
Overall
CADD	15.72	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.149% Middle Eastern · 9/6,024 alleles

Filtering AF 0.0779% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0581%

Overall 0.016% 255/1,596,700 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.359%	278
Middle Easterngrpmax	0.149%	669
Remaining individualsnot grpmax-eligible	0.0452%	2,210
Admixed American	0.0383%	2,609
African / African-American	0.00802%	12,462
European (non-Finnish)	0.00696%	14,372
South Asian	0.00221%	45,332

Ashkenazi Jewish 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: CGN
Protein: p.Thr1069Ala
Coding: c.3205A>G
MANE Select: NM_020770
dbSNP: rs77261959
Type: single nucleotide variant
Location: chr1:151536244 (GRCh38)
Gene constraint: LOEUF 0.88 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.44

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

Similar variants

CGN p.Ala357= Benign/Likely benign ★★ same type
CGN p.Arg11Trp Likely benign ★★ same type
CGN p.Arg227Trp Likely benign ★★ same type
CGN p.Arg547Lys Benign ★★ same type
CGN p.Arg973Gln Benign ★★ same type
CGN p.Glu771Lys Benign/Likely benign ★★ same type
CGN p.Ile60= Benign ★★ same type
CGN p.Ala1035Thr 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/cgn-p-thr1069ala (accessed [today's date]).

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