Is MDFIC p.Phe179= (c.537C>T) pathogenic?

MDFIC p.Phe179= (c.537C>T) is classified Likely benign in MDFIC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-22). Absent from gnomAD v4.1.

How common is MDFIC p.Phe179= (c.537C>T) in the general population?

MDFIC p.Phe179= (c.537C>T) is absent from gnomAD v4.1 (gnomAD).

MDFIC p.Phe179=

c.537C>T · VCV4897546

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP -0.51, phastCons 1
Overall
CADD	8.761	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: MDFIC
Protein: p.Phe179=
Coding: c.537C>T
MANE Select: NM_001166345
Type: single nucleotide variant
Location: chr7:115015731 (GRCh38)
Gene constraint: LOEUF 1.501 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 53.05 · 5 PDB
Residue 179: the mdfi domain; a UniProt-annotated variant site (in lmphm12)

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

Similar variants

MDFIC p.Phe244Leu Uncertain significance ★★ ⚠ same type
MDFIC p.Gly116Arg Likely benign ★★ same type
MDFIC p.Ser60Phe Likely benign ★★ same type
MDFIC p.Ser66= Likely benign ★★ same type
MDFIC c.-188G>C Uncertain significance ★ same type
MDFIC c.-246C>T Uncertain significance ★ same type
MDFIC c.-24G>T Uncertain significance ★ same type
MDFIC c.-269T>A 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/mdfic-p-phe179 (accessed [today's date]).

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