Is ACCSL p.Arg350= (c.1050G>A) pathogenic?

ACCSL p.Arg350= (c.1050G>A) is classified Likely benign in ACCSL (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-31). Ultra-rare (popmax 0.0761%, eas).

How common is ACCSL p.Arg350= (c.1050G>A) in the general population?

ACCSL p.Arg350= (c.1050G>A) is ultra-rare (popmax 0.0761%, eas) (gnomAD).

ACCSL p.Arg350=

c.1050G>A · rs148721026 · VCV2566545

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0761%, eas)

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	GERP -3.5, phastCons 0.46
Overall
CADD	5.815	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0761% East Asian · 34/44,674 alleles

Filtering AF 0.0559% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.049%

Overall 0.00488% 78/1,599,498 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0761%	1,314
South Asian	0.0355%	2,817
Remaining individualsnot grpmax-eligible	0.0178%	5,625
European (non-Finnish)	8.56e-05%	1,168,028

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: ACCSL
Protein: p.Arg350=
Coding: c.1050G>A
MANE Select: NM_001031854
dbSNP: rs148721026
Type: single nucleotide variant
Location: chr11:44055202 (GRCh38)
Gene constraint: LOEUF 1.037 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.52

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

Similar variants

ACCSL p.Ala111Val Uncertain significance ★ ⚠ same type
ACCSL p.Ala248Val Uncertain significance ★ ⚠ same type
ACCSL p.Ala460Val Uncertain significance ★ ⚠ same type
ACCSL p.Ala87Val Uncertain significance ★ ⚠ same type
ACCSL p.Arg102Ser Uncertain significance ★ ⚠ same type
ACCSL p.Arg133His Uncertain significance ★ ⚠ same type
ACCSL p.Arg138Cys Uncertain significance ★ ⚠ same type
ACCSL p.Arg214Gln 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/accsl-p-arg350 (accessed [today's date]).

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