Is HADHB p.Phe310= (c.930C>T) pathogenic?

HADHB p.Phe310= (c.930C>T) is classified Likely benign in HADHB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-03). Absent from gnomAD v4.1; Associated with mitochondrial trifunctional protein deficiency.

What condition is associated with HADHB p.Phe310= (c.930C>T)?

HADHB p.Phe310= (c.930C>T) is associated with mitochondrial trifunctional protein deficiency (ClinVar).

How common is HADHB p.Phe310= (c.930C>T) in the general population?

HADHB p.Phe310= (c.930C>T) is absent from gnomAD v4.1 (gnomAD).

HADHB p.Phe310=

Q: How is Mitochondrial trifunctional protein deficiency inherited?

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

c.930C>T · rs867252047 · VCV2757601

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

mitochondrial trifunctional protein deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.38 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.1	GERP 1.2, phastCons 1
Overall
CADD	10.39	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: HADHB
Protein: p.Phe310=
Coding: c.930C>T
MANE Select: NM_000183
dbSNP: rs867252047
Type: single nucleotide variant
Location: chr2:26280112 (GRCh38)
Gene constraint: LOEUF 1.145 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.89 · 3 PDB

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

Disease context

mitochondrial trifunctional protein deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mitochondrial trifunctional protein deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

HADHB p.Phe310Leu Uncertain significance ★ ⚠ same residue
HADHB c.1149+2T>C Likely pathogenic ★★ same condition
HADHB c.1150-1G>T Likely pathogenic ★★ same condition
HADHB c.1389+5G>A Pathogenic/Likely pathogenic ★★ same condition
HADHB c.209+1G>C Pathogenic ★★ same condition
HADHB c.210-1G>T Pathogenic/Likely pathogenic ★★ same condition
HADHB c.254+1G>A Pathogenic/Likely pathogenic ★★ same condition
HADHB c.255-2A>G 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/hadhb-p-phe310 (accessed [today's date]).

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