Is ARMC5 p.Lys13= (c.39G>A) pathogenic?

ARMC5 p.Lys13= (c.39G>A) is classified Uncertain significance in ARMC5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-26). Very rare (popmax 0.00239%, sas); Associated with ARMC5-related disorder.

What condition is associated with ARMC5 p.Lys13= (c.39G>A)?

ARMC5 p.Lys13= (c.39G>A) is associated with ARMC5-related disorder (ClinVar).

How common is ARMC5 p.Lys13= (c.39G>A) in the general population?

ARMC5 p.Lys13= (c.39G>A) is very rare (popmax 0.00239%, sas) (gnomAD).

ARMC5 p.Lys13=

c.39G>A · rs761201073 · VCV2636753

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00239%, sas)

Conditions

ARMC5-related disorder

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
Constraint at this position
Conservation	phyloP -0.029	GERP -4.3
Overall
CADD	3.999	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00239% South Asian · 2/83,508 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00112%

Overall 0.00169% 26/1,535,368 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00239%	41,754
European (non-Finnish)	0.00201%	49,861
Remaining individualsnot grpmax-eligible	0.00167%	59,978

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ARMC5
Protein: p.Lys13=
Coding: c.39G>A
dbSNP: rs761201073
Type: single nucleotide variant
Location: chr16:31459340 (GRCh38)

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

Disease context

ARMC5-related disorder

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-lys13 (accessed [today's date]).

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