Is ST7 p.Arg150= (c.450G>A) pathogenic?

ST7 p.Arg150= (c.450G>A) is classified Likely benign in ST7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-17). Ultra-rare (popmax 0.018%, eas).

How common is ST7 p.Arg150= (c.450G>A) in the general population?

ST7 p.Arg150= (c.450G>A) is ultra-rare (popmax 0.018%, eas) (gnomAD).

ST7 p.Arg150=

c.450G>A · VCV3322969

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.018%, 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 2.2	GERP -2.4, phastCons 1
Overall
CADD	12.95	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.018% East Asian · 8/44,554 alleles

Filtering AF 0.00889% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00645%

Overall 0.00055% 8/1,453,298 alleles · ultra-rare

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: ST7
Protein: p.Arg150=
Coding: c.450G>A
MANE Select: NM_001369598
Type: single nucleotide variant
Location: chr7:117130491 (GRCh38)
Gene constraint: LOEUF 0.52 · pLI 0.92 (gnomAD)
Structure: AlphaFold pLDDT 80.60

Full ST7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ST7 p.Arg150Trp Uncertain significance ★ ⚠ same residue
ST7 c.1638+860G>T Likely benign ★★ same type
ST7 c.1638+917G>T Likely benign ★★ same type
ST7 c.1638+799A>T Uncertain significance ★ ⚠ same type
ST7 c.1638+818C>T Uncertain significance ★ ⚠ same type
ST7 c.1638+859C>T Uncertain significance ★ ⚠ same type
ST7 c.1638+880A>G Uncertain significance ★ ⚠ same type
ST7 c.1638+887C>T 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/st7-p-arg150 (accessed [today's date]).

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