Is MYRF p.Pro155Ser (c.463C>T) pathogenic?

MYRF p.Pro155Ser (c.463C>T) is classified Uncertain significance in MYRF (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-12). AlphaMissense: likely benign (0.0755); Absent from gnomAD v4.1; Associated with encephalitis/encephalopathy, mild, with reversible myelin vacuolization.

What condition is associated with MYRF p.Pro155Ser (c.463C>T)?

MYRF p.Pro155Ser (c.463C>T) is associated with encephalitis/encephalopathy, mild, with reversible myelin vacuolization (ClinVar).

How common is MYRF p.Pro155Ser (c.463C>T) in the general population?

MYRF p.Pro155Ser (c.463C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MYRF p.Pro155Ser (c.463C>T)?

AlphaMissense predicts likely benign (score 0.0755) — an in-silico prediction, not a clinical call.

MYRF p.Pro155Ser

c.463C>T · rs1055552048 · VCV1027689

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0755 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,604,406)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

encephalitis/encephalopathy, mild, with reversible myelin vacuolization

Computational evidence

Protein change
AlphaMissense	0.0755	likely benign
REVEL	0.137	moderately benign-leaning
SaProt	LLR -6.22	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP 1.7, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 19 kb · p 0.074 · regional, not allelic
Overall
CADD	21.0	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

No allele count reported in gnomAD v4.1 (AN 1,604,406). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MYRF
Protein: p.Pro155Ser
Coding: c.463C>T
MANE Select: NM_001127392
dbSNP: rs1055552048
Type: single nucleotide variant
Location: chr11:61770248 (GRCh38)
Gene constraint: LOEUF 0.215 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 61.76 · 2 PDB

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

Disease context

encephalitis/encephalopathy, mild, with reversible myelin vacuolization — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MYRF p.Ala1001Ser Uncertain significance ★★ ⚠ same condition
MYRF p.Glu421Lys Uncertain significance ★★ ⚠ same condition
MYRF p.Thr892Ala Uncertain significance ★★ ⚠ same condition
MYRF p.Gln515Ter Pathogenic ★ same condition
MYRF c.2764+3A>G Uncertain significance ★ same condition
MYRF c.3301-13C>T Uncertain significance ★ same condition
MYRF p.Arg983Gly Uncertain significance ★ ⚠ same condition
MYRF p.Asn691Ile 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/myrf-p-pro155ser (accessed [today's date]).

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