Is ST7 p.Ser564Arg (c.1690A>C) pathogenic?

ST7 p.Ser564Arg (c.1690A>C) is classified Uncertain significance in ST7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-17). Absent from gnomAD v4.1.

How common is ST7 p.Ser564Arg (c.1690A>C) in the general population?

ST7 p.Ser564Arg (c.1690A>C) is absent from gnomAD v4.1 (gnomAD).

ST7 p.Ser564Arg

c.1690A>C · VCV4897563

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.218	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.4	GERP 2.3, phastCons 1
Regional constraint	o/e 0.54	unconstrained · MANE · 110 kb · p 6e-27 · regional, not allelic
Overall
CADD	24.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ST7
Protein: p.Ser564Arg
Coding: c.1690A>C
MANE Select: NM_001369598
Type: single nucleotide variant
Location: chr7:117229813 (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.Ser564Gly 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-ser564arg (accessed [today's date]).

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