Is SLC45A2 p.Val73= (c.219G>A) pathogenic?

SLC45A2 p.Val73= (c.219G>A) is classified Likely benign in SLC45A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-28). Absent from gnomAD v4.1.

How common is SLC45A2 p.Val73= (c.219G>A) in the general population?

SLC45A2 p.Val73= (c.219G>A) is absent from gnomAD v4.1 (gnomAD).

SLC45A2 p.Val73=

c.219G>A · rs367766561 · VCV2903728

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 assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.82	GERP 1.2, phastCons 1
Overall
CADD	10.38	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: SLC45A2
Protein: p.Val73=
Coding: c.219G>A
MANE Select: NM_016180
dbSNP: rs367766561
Type: single nucleotide variant
Location: chr5:33984365 (GRCh38)
Gene constraint: LOEUF 1.022 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.96

Full SLC45A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SLC45A2 p.Val73Glu Uncertain significance ★★ ⚠ same residue
SLC45A2 p.Val73Gly Uncertain significance ★ ⚠ same residue
SLC45A2 p.Val73Leu Uncertain significance ★ ⚠ same residue
SLC45A2 p.Val73Met Uncertain significance ★ ⚠ same residue
SLC45A2 c.1156+1G>C Pathogenic/Likely pathogenic ★★ same type
SLC45A2 c.386-1G>A Pathogenic ★★ same type
SLC45A2 p.Ala486Thr Pathogenic/Likely pathogenic ★★ same type
SLC45A2 p.Ala511Glu Pathogenic ★★ 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/slc45a2-p-val73 (accessed [today's date]).

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