Is MEF2C p.Arg464= (c.1392C>T) pathogenic?

MEF2C p.Arg464= (c.1392C>T) is classified Likely benign in MEF2C (ClinVar, Single submitter, 1 submitter; last evaluated 2017-05-11). Absent from gnomAD v4.1.

How common is MEF2C p.Arg464= (c.1392C>T) in the general population?

MEF2C p.Arg464= (c.1392C>T) is absent from gnomAD v4.1 (gnomAD).

MEF2C p.Arg464=

c.1392C>T · rs1554098511 · VCV509393

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Pangolin	Δ0.48	gain · loss 0.00 · independent
Constraint at this position
Conservation	phyloP 10	GERP 2.4, phastCons 1
Overall
CADD	14.61	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: MEF2C
Protein: p.Arg464=
Coding: c.1392C>T
MANE Select: NM_002397
dbSNP: rs1554098511
Type: single nucleotide variant
Location: chr5:88722634 (GRCh38)

Full MEF2C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/mef2c-p-arg464 (accessed [today's date]).

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