Is MITF p.Glu520Lys (c.1558G>A) pathogenic?

MITF p.Glu520Lys (c.1558G>A) is classified Uncertain significance in MITF (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-12-08). AlphaMissense: ambiguous (0.4767); Very rare (popmax 8.48e-05%, nfe); Associated with Tietz syndrome.

What condition is associated with MITF p.Glu520Lys (c.1558G>A)?

MITF p.Glu520Lys (c.1558G>A) is associated with Tietz syndrome, Waardenburg syndrome type 2A, melanoma, cutaneous malignant, susceptibility to, 8 (ClinVar).

How common is MITF p.Glu520Lys (c.1558G>A) in the general population?

MITF p.Glu520Lys (c.1558G>A) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about MITF p.Glu520Lys (c.1558G>A)?

AlphaMissense predicts ambiguous (score 0.4767) — an in-silico prediction, not a clinical call.

MITF p.Glu520Lys

c.1558G>A · rs1193602968 · VCV1977704

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

ambiguous

0.4767 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Conditions

Tietz syndrome

Computational evidence

Protein change
AlphaMissense	0.4767	ambiguous
REVEL	0.436	indeterminate
SaProt	LLR -8.14	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.1, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 5,907 bp · p 0.32 · regional, not allelic
Overall
CADD	29.5	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,846 alleles

Overall 6.2e-05% 1/1,613,928 alleles · very rare exomes 1/1,461,626 · genomes 0/152,302 · joint denominator

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: MITF
Protein: p.Glu520Lys
Coding: c.1558G>A
MANE Select: NM_001354604
dbSNP: rs1193602968
Type: single nucleotide variant
Location: chr3:69965225 (GRCh38)
Gene constraint: LOEUF 0.482 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 62.25 · 12 PDB
Residue 520: the 'disordered' region

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

Disease context

Tietz syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Waardenburg syndrome type 2A melanoma, cutaneous malignant, susceptibility to, 8 hereditary neoplastic syndrome

Similar variants

MITF p.Glu520Asp Uncertain significance ★★ ⚠ same residue
MITF p.Glu520Val Uncertain significance ★ same residue
MITF c.1031+1G>A Pathogenic ★★ same condition
MITF c.1179+1G>A Pathogenic ★★ same condition
MITF c.355-1062G>C Pathogenic/Likely pathogenic ★★ same condition
MITF c.880+1G>A Likely pathogenic ★★ same condition
MITF c.955+1G>A Likely pathogenic ★★ same condition
MITF c.956-1G>A Pathogenic ★★ 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/mitf-p-glu520lys (accessed [today's date]).

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