Is ARMC5 p.Pro501fs (c.1502del) pathogenic?

ARMC5 p.Pro501fs (c.1502del) is classified Likely pathogenic in ARMC5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-23). Absent from gnomAD; Associated with ARMC5-related disorder.

What condition is associated with ARMC5 p.Pro501fs (c.1502del)?

ARMC5 p.Pro501fs (c.1502del) is associated with ARMC5-related disorder (ClinVar).

How common is ARMC5 p.Pro501fs (c.1502del) in the general population?

ARMC5 p.Pro501fs (c.1502del) is absent from gnomAD (gnomAD).

ARMC5 p.Pro501fs

c.1502del · rs2544859360 · VCV2632699

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ARMC5-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -4.3	GERP -3.4

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: ARMC5
Protein: p.Pro501fs
Coding: c.1502del
MANE Select: NM_001105247
dbSNP: rs2544859360
Type: Deletion
Location: chr16:31464524 (GRCh38)
Gene constraint: LOEUF 0.772 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.27
Residue 501: the 'disordered' region; a UniProt-annotated variant site (in aimah2; uncertain significance); a UniProt-annotated variant site (in aimah2)

Full ARMC5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ARMC5-related disorder

Similar variants

ARMC5 p.Pro501Leu Uncertain significance ★ ⚠ same residue
ARMC5 p.Gly108fs Likely pathogenic ★ same condition
ARMC5 p.Pro602fs Likely pathogenic ★ same condition
ARMC5 p.Pro731fs Likely pathogenic ★ same condition
ARMC5 p.Val201fs Likely pathogenic ★ same condition
ARMC5 p.Pro501= Likely benign ★ same residue
ARMC5 p.Arg173Ter Pathogenic ★★ same condition
ARMC5 p.Arg690Gln Uncertain significance ★★ ⚠ 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/armc5-p-pro501fs (accessed [today's date]).

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