Is SLC52A1 p.Pro73= (c.219G>A) pathogenic?

SLC52A1 p.Pro73= (c.219G>A) is classified Likely benign in SLC52A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-02). Ultra-rare (popmax 0.0184%, nfe); Associated with Vitamin B2 deficiency.

What condition is associated with SLC52A1 p.Pro73= (c.219G>A)?

SLC52A1 p.Pro73= (c.219G>A) is associated with Vitamin B2 deficiency (ClinVar).

How common is SLC52A1 p.Pro73= (c.219G>A) in the general population?

SLC52A1 p.Pro73= (c.219G>A) is ultra-rare (popmax 0.0184%, nfe) (gnomAD).

SLC52A1 p.Pro73=

c.219G>A · rs201983129 · VCV1083484

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0184%, nfe)

Conditions

Vitamin B2 deficiency

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 -4.3	GERP -3.4
Overall
CADD	13.28	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0184% European (non-Finnish) · 217/1,177,354 alleles

Filtering AF 0.0164% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0156%

Overall 0.0152% 244/1,609,574 alleles · ultra-rare exomes 227/1,457,296 · genomes 17/152,278 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0184%	5,426
African / African-American	0.016%	6,246
Remaining individualsnot grpmax-eligible	0.0145%	6,919
East Asian	0.00669%	14,946
South Asian	0.00221%	45,339
Admixed American	0.00168%	59,676

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: SLC52A1
Protein: p.Pro73=
Coding: c.219G>A
MANE Select: NM_017986
dbSNP: rs201983129
Type: single nucleotide variant
Location: chr17:5034270 (GRCh38)
Gene constraint: LOEUF 1.121 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.13

Full SLC52A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Vitamin B2 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SLC52A1 p.Pro73Leu Uncertain significance ★ ⚠ same residue
SLC52A1 p.Ala175Val Uncertain significance ★★ ⚠ same condition
SLC52A1 p.Ala250Thr Uncertain significance ★★ ⚠ same condition
SLC52A1 p.Ala323Thr Uncertain significance ★★ ⚠ same condition
SLC52A1 p.Arg145Gln Uncertain significance ★★ ⚠ same condition
SLC52A1 p.Arg169His Uncertain significance ★★ ⚠ same condition
SLC52A1 p.Arg190Cys Uncertain significance ★★ ⚠ same condition
SLC52A1 p.Arg190His Uncertain significance ★★ ⚠ same condition

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/slc52a1-p-pro73 (accessed [today's date]).

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