Is MRTFA p.Pro898fs (c.2693_2711del) pathogenic?

MRTFA p.Pro898fs (c.26932711del) is classified Uncertain significance in MRTFA (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-13). No gnomAD frequency available for this variant.

How common is MRTFA p.Pro898fs (c.2693_2711del) in the general population?

MRTFA p.Pro898fs (c.2693_2711del) is no gnomAD frequency available for this variant (gnomAD).

MRTFA p.Pro898fs

c.2693_2711del · rs2517787339 · VCV2030248

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	escapes	premature termination codon in the last exon (15 of 15) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -7.1	GERP -4.2

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MRTFA
Protein: p.Pro898fs
Coding: c.2693_2711del
MANE Select: NM_020831
dbSNP: rs2517787339
Type: Deletion
Location: chr22:40411775 (GRCh38)
Gene constraint: LOEUF 0.389 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 56.59 · 2 PDB
Residue 898: a UniProt-annotated variant site (in imd66; probable loss-of-function; patient's dendritic cells are morphologically distinct from control dendritic cells and show reduced spreading on fibronectin-coated coverslips, a marked reduction in total f-actin staining and a complete absence of podosomes, a similar phenotype to that of thp1 cells in which mrtfa was silenced)

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

Similar variants

MRTFA p.Pro898Ser Uncertain significance ★★ ⚠ same residue
MRTFA p.Pro898Leu Uncertain significance ★ ⚠ same residue
MRTFA c.2518-15del Benign/Likely benign ★★ same type
MRTFA c.2365-26_2365-19del Uncertain significance ★ same type
MRTFA p.Ala523_Val531del Uncertain significance ★ same type
MRTFA p.Glu658del Uncertain significance ★ same type
MRTFA p.Glu678del Uncertain significance ★ same type
MRTFA p.Glu875del 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/mrtfa-p-pro898fs (accessed [today's date]).

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