Is SLC19A1 p.Asp56Asn (c.166G>A) pathogenic?

SLC19A1 p.Asp56Asn (c.166G>A) is classified Uncertain significance in SLC19A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-10). AlphaMissense: likely benign (0.1082); Rare (popmax 0.442%, eas).

How common is SLC19A1 p.Asp56Asn (c.166G>A) in the general population?

SLC19A1 p.Asp56Asn (c.166G>A) is rare (popmax 0.442%, eas) (gnomAD).

What do computational predictors say about SLC19A1 p.Asp56Asn (c.166G>A)?

AlphaMissense predicts likely benign (score 0.1082) — an in-silico prediction, not a clinical call.

SLC19A1 p.Asp56Asn

c.166G>A · rs146321452 · VCV2882495

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1082 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.442%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1082	likely benign
REVEL	0.223	benign-leaning
SaProt	LLR -8.50	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -1.1	GERP -2.8
Regional constraint	o/e 1.00	unconstrained · MANE · 22 kb · p 0.89 · regional, not allelic
Overall
CADD	17.14	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.442% East Asian · 132/29,844 alleles

Filtering AF 0.381% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.358%

Overall 0.0137% 195/1,425,656 alleles · rare exomes 155/1,284,236 · genomes 40/141,420 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.442%	226
African / African-American	0.0671%	1,490
Remaining individualsnot grpmax-eligible	0.00771%	12,967
Admixed American	0.00204%	49,126
European (non-Finnish)	0.00121%	82,338
South Asian	0.00121%	82,452

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: SLC19A1
Protein: p.Asp56Asn
Coding: c.166G>A
MANE Select: NM_194255
dbSNP: rs146321452
Type: single nucleotide variant
Location: chr21:45537794 (GRCh38)
Gene constraint: LOEUF 1.585 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.30 · 19 PDB
Residue 56: a turn

Full SLC19A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SLC19A1 p.Asp56His Benign/Likely benign ★★ same residue
COL18A1 p.Arg1081Ter Pathogenic/Likely pathogenic ★★ same type
COL18A1 p.Arg915Ter Pathogenic/Likely pathogenic ★★ same type
RFC1 p.Arg383Ter Pathogenic/Likely pathogenic ★★ same type
COL18A1 c.*30G>A Uncertain significance ★★ same type
COL18A1 p.Ala1089Thr Uncertain significance ★★ ⚠ same type
COL18A1 p.Ala1254Val Uncertain significance ★★ ⚠ same type
COL18A1 p.Arg1081Gln 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/slc19a1-p-asp56asn (accessed [today's date]).

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