Is SLC2A9 p.Asp7= (c.21C>T) pathogenic?

SLC2A9 p.Asp7= (c.21C>T) is classified Likely benign in SLC2A9 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-02-01). Rare (popmax 0.397%, nfe).

How common is SLC2A9 p.Asp7= (c.21C>T) in the general population?

SLC2A9 p.Asp7= (c.21C>T) is rare (popmax 0.397%, nfe) (gnomAD).

SLC2A9 p.Asp7=

c.21C>T · rs144215444 · VCV2654664

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.397%, nfe)

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 0.47	GERP -1.9
Overall
CADD	11.74	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.397% European (non-Finnish) · 4,679/1,179,720 alleles

Filtering AF 0.387% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.383%

Overall 0.322% 5,197/1,613,744 alleles · rare exomes 4,837/1,461,524 · genomes 360/152,220 · joint denominator

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	0.548%	182
European (non-Finnish)grpmax	0.397%	252
Remaining individualsnot grpmax-eligible	0.266%	376
South Asian	0.133%	753
Admixed American	0.128%	779
Finnishnot grpmax-eligible	0.116%	865
Ashkenazi Jewishnot grpmax-eligible	0.0878%	1,138
African / African-American	0.0653%	1,531

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: SLC2A9
Protein: p.Asp7=
Coding: c.21C>T
MANE Select: NM_020041 · reported on NM_001001290
dbSNP: rs144215444
Type: single nucleotide variant
Location: chr4:10025946 (GRCh38)
Gene constraint: LOEUF 1.022 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.79 · 7 PDB
Residue 7: the 'disordered' region

Full SLC2A9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SLC2A9 c.681+1G>T Likely pathogenic ★★ same type
SLC2A9 p.Leu75Arg Pathogenic/Likely pathogenic ★★ same type
SLC2A9 p.Thr125Met Likely pathogenic ★★ ⚠ same type
SLC2A9 p.Arg380Gln Uncertain significance ★★ ⚠ same type
SLC2A9 p.Arg447Trp Uncertain significance ★★ ⚠ same type
SLC2A9 p.Asn144Ser Uncertain significance ★★ ⚠ same type
SLC2A9 p.Ile149Val Uncertain significance ★★ ⚠ same type
SLC2A9 p.Ile207Val 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/slc2a9-p-asp7 (accessed [today's date]).

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