Is TYMP p.Phe164Val (c.490T>G) pathogenic?

TYMP p.Phe164Val (c.490T>G) is classified Uncertain significance in TYMP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2025-05-08). AlphaMissense: likely pathogenic (0.6408); Absent from gnomAD v4.1; Associated with mitochondrial neurogastrointestinal encephalomyopathy.

What condition is associated with TYMP p.Phe164Val (c.490T>G)?

TYMP p.Phe164Val (c.490T>G) is associated with mitochondrial neurogastrointestinal encephalomyopathy (ClinVar).

How common is TYMP p.Phe164Val (c.490T>G) in the general population?

TYMP p.Phe164Val (c.490T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TYMP p.Phe164Val (c.490T>G)?

AlphaMissense predicts likely pathogenic (score 0.6408) — an in-silico prediction, not a clinical call.

TYMP p.Phe164Val

Q: How is Mitochondrial neurogastrointestinal encephalomyopathy inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.490T>G · VCV4062462

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6408 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

mitochondrial neurogastrointestinal encephalomyopathy

Computational evidence

Protein change
AlphaMissense	0.6408	likely pathogenic
REVEL	0.956	strongly pathogenic-leaning
SaProt	LLR -8.93	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2, phastCons 1
Regional constraint	o/e 1.24	unconstrained · MANE · 3,936 bp · p 9.1e-10 · regional, not allelic
Overall
CADD	25.1	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

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: TYMP
Protein: p.Phe164Val
Coding: c.490T>G
MANE Select: NM_001953
Type: single nucleotide variant
Location: chr22:50528538 (GRCh38)
Gene constraint: LOEUF 1.518 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.82 · 4 PDB

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

Disease context

mitochondrial neurogastrointestinal encephalomyopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mitochondrial neurogastrointestinal encephalomyopathy (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

TYMP p.Phe164Tyr Uncertain significance ★ ⚠ same residue
TYMP c.1301-1G>A Likely pathogenic ★★ same condition
TYMP c.418-1G>A Likely pathogenic ★★ same condition
TYMP p.Ala216Val Likely pathogenic ★★ same condition
TYMP p.Asp114Asn Likely pathogenic ★★ same condition
TYMP p.Glu21Ter Pathogenic/Likely pathogenic ★★ same condition
TYMP p.Glu289Ala Pathogenic ★★ same condition
TYMP p.Gly145Arg Pathogenic/Likely 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/tymp-p-phe164val (accessed [today's date]).

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