Is SLC18A3 p.Pro80= (c.240C>T) pathogenic?

SLC18A3 p.Pro80= (c.240C>T) is classified Likely benign in SLC18A3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-07). Absent from gnomAD v4.1.

How common is SLC18A3 p.Pro80= (c.240C>T) in the general population?

SLC18A3 p.Pro80= (c.240C>T) is absent from gnomAD v4.1 (gnomAD).

SLC18A3 p.Pro80=

c.240C>T · rs2132685994 · VCV1617613

Likely benign Single submitter

Classification

Likely benign

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.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.9	GERP 0.69, phastCons 1
Overall
CADD	11.22	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: SLC18A3
Protein: p.Pro80=
Coding: c.240C>T
MANE Select: NM_020549 · reported on NM_003055
dbSNP: rs2132685994
Type: single nucleotide variant
Location: chr10:49610980 (GRCh38)

Full SLC18A3 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/slc18a3-p-pro80 (accessed [today's date]).

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