Is MTTP p.Glu462Val (c.1385A>T) pathogenic?

MTTP p.Glu462Val (c.1385A>T) is classified Uncertain significance in MTTP (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-01-09). AlphaMissense: likely benign (0.173); Rare (popmax 0.1%, mid); Associated with abetalipoproteinemia.

What condition is associated with MTTP p.Glu462Val (c.1385A>T)?

MTTP p.Glu462Val (c.1385A>T) is associated with abetalipoproteinemia, metabolic syndrome X (ClinVar).

How common is MTTP p.Glu462Val (c.1385A>T) in the general population?

MTTP p.Glu462Val (c.1385A>T) is rare (popmax 0.1%, mid) (gnomAD).

How is Abetalipoproteinemia inherited?

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

What do computational predictors say about MTTP p.Glu462Val (c.1385A>T)?

AlphaMissense predicts likely benign (score 0.173) — an in-silico prediction, not a clinical call.

MTTP p.Glu462Val

c.1385A>T · rs757598679 · VCV1381641

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.173 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.1%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

abetalipoproteinemia

Computational evidence

Protein change
AlphaMissense	0.173	likely benign
REVEL	0.246	benign-leaning
SaProt	LLR -9.64	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 9.2	GERP 0.4, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 48 kb · p 0.00018 · regional, not allelic
Overall
CADD	24.9	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

Grpmax group 0.1% Middle Eastern · 6/5,992 alleles

Filtering AF 0.0435% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0297%

Overall 0.00273% 44/1,613,880 alleles · rare exomes 43/1,461,714 · genomes 1/152,166 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.1%	999
Remaining individualsnot grpmax-eligible	0.0032%	31,238
European (non-Finnish)	0.00305%	32,778

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: MTTP
Protein: p.Glu462Val
Coding: c.1385A>T
MANE Select: NM_001386140
dbSNP: rs757598679
Type: single nucleotide variant
Location: chr4:99606788 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.73 · 2 PDB
Residue 462: the vitellogenin domain; an α-helix

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

Disease context

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

Also linked: metabolic syndrome X

For Abetalipoproteinemia (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy
Prevalence: <1 / 1 000 000 (Worldwide)

Similar variants

MTTP p.Glu462fs Likely pathogenic ★★ same residue
MTTP c.1067+1G>C Likely pathogenic ★★ same condition
MTTP c.1769+2T>C Pathogenic/Likely pathogenic ★★ same condition
MTTP c.1867+1G>A Pathogenic ★★ same condition
MTTP c.1867+5G>A Pathogenic/Likely pathogenic ★★ same condition
MTTP c.1868-2A>G Likely pathogenic ★★ same condition
MTTP c.2342+1G>A Pathogenic ★★ same condition
MTTP c.502-1G>C 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/mttp-p-glu462val (accessed [today's date]).

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