Is STRA6 p.Arg19= (c.57G>A) pathogenic?

STRA6 p.Arg19= (c.57G>A) is classified Likely benign in STRA6 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-09-12). Ultra-rare (popmax 0.0591%, nfe).

How common is STRA6 p.Arg19= (c.57G>A) in the general population?

STRA6 p.Arg19= (c.57G>A) is ultra-rare (popmax 0.0591%, nfe) (gnomAD).

STRA6 p.Arg19=

c.57G>A · rs184924574 · VCV3035399

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0591%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.14	GERP -0.038, phastCons 0.004
Overall
CADD	11.37	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0591% European (non-Finnish) · 678/1,146,874 alleles

Filtering AF 0.0553% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0539%

Overall 0.0531% 816/1,535,646 alleles · ultra-rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.251%	398
Remaining individualsnot grpmax-eligible	0.0683%	1,464
European (non-Finnish)grpmax	0.0591%	1,692
Admixed American	0.0353%	2,834
African / African-American	0.0082%	12,193
South Asian	0.00119%	84,050

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: STRA6
Protein: p.Arg19=
Coding: c.57G>A
MANE Select: NM_025055 · reported on NM_001199040
dbSNP: rs184924574
Type: single nucleotide variant
Location: chr15:74209398 (GRCh38)

Full STRA6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/stra6-p-arg19 (accessed [today's date]).

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