Is ATN1 p.Arg810= (c.2430C>A) pathogenic?

ATN1 p.Arg810= (c.2430C>A) is classified Benign in ATN1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2021-11-29). Common (popmax 35.7%, nfe) — too common for a highly-penetrant pathogenic allele.

ATN1 p.Arg810=

Q: How common is ATN1 p.Arg810= (c.2430C>A) in the general population?

ATN1 p.Arg810= (c.2430C>A) is common (popmax 35.7%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2430C>A · rs7969685 · VCV128462

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 35.7%, nfe) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP -1.8, phastCons 1
Overall
CADD	13.37	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 35.7% European (non-Finnish) · 410,556/1,148,948 alleles

Filtering AF 35.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 35.6%

Overall 31.9% 495,295/1,552,886 alleles · common

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	37.1%	3
European (non-Finnish)grpmax	35.7%	3
Finnishnot grpmax-eligible	32.6%	3
Middle Eastern	30.7%	3
Remaining individualsnot grpmax-eligible	29.4%	3
South Asian	19.3%	5
Admixed American	18.6%	5
Amishnot grpmax-eligible	17.1%	6
African / African-American	12.9%	8
East Asian	0.173%	577

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: ATN1
Protein: p.Arg810=
Coding: c.2430C>A
MANE Select: NM_001940
dbSNP: rs7969685
Type: single nucleotide variant
Location: chr12:6937980 (GRCh38)
Gene constraint: LOEUF 0.352 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 49.25
Residue 810: the 'disordered' region

Full ATN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ATN1 p.His1052Pro Pathogenic/Likely pathogenic ★★ same type
ATN1 p.Ser1059Leu Pathogenic/Likely pathogenic ★★ same type
ATN1 p.Arg1152Cys Uncertain significance ★★ ⚠ same type
ATN1 p.Asn422Ser Uncertain significance ★★ ⚠ same type
ATN1 p.Glu814Gly Uncertain significance ★★ ⚠ same type
ATN1 p.Met335Ile Uncertain significance ★★ ⚠ same type
ATN1 p.Pro185Ala Uncertain significance ★★ ⚠ same type
ATN1 p.Pro720Ser 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/atn1-p-arg810 (accessed [today's date]).

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