Is SLC18A2 p.Val9= (c.27C>T) pathogenic?

SLC18A2 p.Val9= (c.27C>T) is classified Likely benign in SLC18A2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-05-01). Rare (popmax 0.849%, mid).

How common is SLC18A2 p.Val9= (c.27C>T) in the general population?

SLC18A2 p.Val9= (c.27C>T) is rare (popmax 0.849%, mid) (gnomAD).

SLC18A2 p.Val9=

c.27C>T · rs368087382 · VCV747914

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.849%, mid)

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 -1.2	GERP -4
Overall
CADD	15.88	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.849% Middle Eastern · 46/5,416 alleles

Filtering AF 0.654% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.585%

Overall 0.0144% 231/1,604,790 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.849%	118
Remaining individualsnot grpmax-eligible	0.0483%	2,069
Admixed American	0.0186%	5,386
South Asian	0.0111%	9,000
European (non-Finnish)	0.0108%	9,266
African / African-American	0.00804%	12,433
East Asian	0.00226%	44,310

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: SLC18A2
Protein: p.Val9=
Coding: c.27C>T
dbSNP: rs368087382
Type: single nucleotide variant
Location: chr10:117241720 (GRCh38)

Full SLC18A2 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/slc18a2-p-val9 (accessed [today's date]).

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