Is AGA p.Asp205= (c.615C>T) pathogenic?

AGA p.Asp205= (c.615C>T) is classified Likely benign in AGA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-06). Very rare (popmax 6.22e-05%); Associated with Inborn genetic diseases.

What condition is associated with AGA p.Asp205= (c.615C>T)?

AGA p.Asp205= (c.615C>T) is associated with Inborn genetic diseases (ClinVar).

How common is AGA p.Asp205= (c.615C>T) in the general population?

AGA p.Asp205= (c.615C>T) is very rare (popmax 6.22e-05%) (gnomAD).

AGA p.Asp205=

c.615C>T · VCV4248926

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.22e-05%)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.172	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.47	GERP -3.4, phastCons 0.77
Overall
CADD	4.192	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.22e-05%

Overall 6.22e-05% 1/1,607,110 alleles · very rare exomes 0/1,454,928 · genomes 1/152,182 · joint denominator

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: AGA
Protein: p.Asp205=
Coding: c.615C>T
MANE Select: NM_000027
Type: single nucleotide variant
Location: chr4:177437412 (GRCh38)
Gene constraint: LOEUF 0.938 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 91.41 · 2 PDB

Full AGA 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

AGA p.Ala285Gly Uncertain significance ★★ ⚠ same condition
AGA p.Asn143Ser Uncertain significance ★★ ⚠ same condition
AGA p.Ala101= Benign/Likely benign ★★ same condition
AGA p.Phe326= Likely benign ★★ same condition
AGA p.Val57= Likely benign ★★ same condition
AGA c.394+1G>A Likely pathogenic ★ same condition
AGA p.Asp261Asn Uncertain significance ★ ⚠ same condition
AGA p.His296Pro 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/aga-p-asp205 (accessed [today's date]).

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