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

SBDS p.Arg19= (c.57G>A) is classified Likely benign in SBDS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-06). Ultra-rare (popmax 0.0173%, afr); Associated with Inborn genetic diseases.

What condition is associated with SBDS p.Arg19= (c.57G>A)?

SBDS p.Arg19= (c.57G>A) is associated with Inborn genetic diseases (ClinVar).

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

SBDS p.Arg19= (c.57G>A) is ultra-rare (popmax 0.0173%, afr) (gnomAD).

SBDS p.Arg19=

c.57G>A · VCV3437538

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0173%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.11	GERP -3.6, phastCons 0.38
Overall
CADD	11.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0173% African / African-American · 13/74,958 alleles

Filtering AF 0.0102% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00812%

Overall 0.000867% 14/1,614,056 alleles · ultra-rare exomes 10/1,461,786 · genomes 4/152,270 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0173%	5,766
European (non-Finnish)	8.47e-05%	1,180,025

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: SBDS
Protein: p.Arg19=
Coding: c.57G>A
MANE Select: NM_016038
Type: single nucleotide variant
Location: chr7:66995361 (GRCh38)
Gene constraint: LOEUF 1.08 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.97 · 6 PDB
Residue 19: a β-strand

Full SBDS 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

SBDS p.Arg19Gly Uncertain significance ★ ⚠ same residue
SBDS p.Lys33Thr Pathogenic/Likely pathogenic ★★ same condition
SBDS p.Arg22Cys Uncertain significance ★★ ⚠ same condition
SBDS p.Asp246Asn Uncertain significance ★★ ⚠ same condition
SBDS p.Cys216Tyr Uncertain significance ★★ ⚠ same condition
SBDS p.Ile111Val Uncertain significance ★★ ⚠ same condition
SBDS p.Ile224Thr Uncertain significance ★★ ⚠ same condition
SBDS p.Lys240Arg 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/sbds-p-arg19 (accessed [today's date]).

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