Is ATIC p.His470Gln (c.1410T>A) pathogenic?

ATIC p.His470Gln (c.1410T>A) is classified Uncertain significance in ATIC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-04). AlphaMissense: likely pathogenic (0.8166); Ultra-rare (popmax 0.0758%, eas).

How common is ATIC p.His470Gln (c.1410T>A) in the general population?

ATIC p.His470Gln (c.1410T>A) is ultra-rare (popmax 0.0758%, eas) (gnomAD).

What do computational predictors say about ATIC p.His470Gln (c.1410T>A)?

AlphaMissense predicts likely pathogenic (score 0.8166) — an in-silico prediction, not a clinical call.

ATIC p.His470Gln

c.1410T>A · VCV3714000

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8166 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0758%, eas)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8166	likely pathogenic
REVEL	0.668	pathogenic-leaning
SaProt	LLR -10.56	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3	GERP -5.6
Regional constraint	o/e 1.07	unconstrained · MANE · 38 kb · p 0.044 · regional, not allelic
Overall
CADD	17.18	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

Grpmax group 0.0758% East Asian · 34/44,884 alleles

Filtering AF 0.0557% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0488%

Overall 0.00514% 83/1,614,174 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0758%	1,320
Remaining individualsnot grpmax-eligible	0.0512%	1,953
South Asian	0.0143%	7,006
African / African-American	0.00267%	37,518
European (non-Finnish)	0.000169%	590,009

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: ATIC
Protein: p.His470Gln
Coding: c.1410T>A
MANE Select: NM_004044
Type: single nucleotide variant
Location: chr2:215346848 (GRCh38)
Gene constraint: LOEUF 1.044 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 97.46 · 5 PDB
Residue 470: the 'aicar formyltransferase' region

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

Similar variants

ATIC p.His470Tyr Uncertain significance ★ ⚠ same residue
ATIC c.688+3A>G Uncertain significance ★★ same type
ATIC p.Ala140Thr Uncertain significance ★★ ⚠ same type
ATIC p.Ala183Glu Uncertain significance ★★ ⚠ same type
ATIC p.Ala510Thr Uncertain significance ★★ ⚠ same type
ATIC p.His584Arg Uncertain significance ★★ ⚠ same type
ATIC p.Ile491Val Uncertain significance ★★ ⚠ same type
ATIC p.Val154Ala 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/atic-p-his470gln (accessed [today's date]).

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