Is MFAP1 p.Glu78Asp (c.234G>C) pathogenic?

MFAP1 p.Glu78Asp (c.234G>C) is classified Uncertain significance in MFAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-05). AlphaMissense: likely benign (0.065); Absent from gnomAD v4.1.

How common is MFAP1 p.Glu78Asp (c.234G>C) in the general population?

MFAP1 p.Glu78Asp (c.234G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MFAP1 p.Glu78Asp (c.234G>C)?

AlphaMissense predicts likely benign (score 0.065) — an in-silico prediction, not a clinical call.

MFAP1 p.Glu78Asp

c.234G>C · VCV4107127

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.065 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.065	likely benign
REVEL	0.198	benign-leaning
SaProt	LLR -7.16	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 -0.73	GERP -3.5, phastCons 0.014
Regional constraint	o/e 0.75	unconstrained · MANE · 7,531 bp · p 5e-06 · regional, not allelic
Overall
CADD	9.607	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

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: MFAP1
Protein: p.Glu78Asp
Coding: c.234G>C
MANE Select: NM_005926
Type: single nucleotide variant
Location: chr15:43817294 (GRCh38)
Gene constraint: LOEUF 0.412 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.84 · 14 PDB
Residue 78: the 'disordered' region

Full MFAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MFAP1 p.Arg306His Uncertain significance ★ ⚠ same type
MFAP1 p.Arg316Lys Uncertain significance ★ ⚠ same type
MFAP1 p.Arg436Gln Uncertain significance ★ ⚠ same type
MFAP1 p.Arg87Gln Uncertain significance ★ ⚠ same type
MFAP1 p.Gln14His Uncertain significance ★ ⚠ same type
MFAP1 p.Glu163Asp Uncertain significance ★ ⚠ same type
MFAP1 p.Glu318Ala Uncertain significance ★ same type
MFAP1 p.Glu98Gly Uncertain significance ★ ⚠ same type

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/mfap1-p-glu78asp (accessed [today's date]).

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