Is ARMCX1 p.Arg5= (c.15G>A) pathogenic?

ARMCX1 p.Arg5= (c.15G>A) is classified Benign in ARMCX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-05-17). Rare (popmax 0.583%, nfe).

How common is ARMCX1 p.Arg5= (c.15G>A) in the general population?

ARMCX1 p.Arg5= (c.15G>A) is rare (popmax 0.583%, nfe) (gnomAD).

ARMCX1 p.Arg5=

c.15G>A · rs142274849 · VCV769182

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.583%, nfe)

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 2	phastCons 1
Overall
CADD	8.428	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.583% European (non-Finnish) · 5,218/894,491 alleles

Filtering AF 0.57% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.565%

Overall 0.475% 5,742/1,208,561 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	1.17%	86
European (non-Finnish)grpmax	0.583%	171
Admixed American	0.46%	218
Remaining individualsnot grpmax-eligible	0.431%	232
Ashkenazi Jewishnot grpmax-eligible	0.146%	684
Finnishnot grpmax-eligible	0.0645%	1,551
African / African-American	0.0593%	1,685
Middle Eastern	0.046%	2,172
South Asian	0.00355%	28,188
East Asian	0.00296%	33,733

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ARMCX1
Protein: p.Arg5=
Coding: c.15G>A
MANE Select: NM_016608
dbSNP: rs142274849
Type: single nucleotide variant
Location: chrX:101552945 (GRCh38)
Structure: AlphaFold pLDDT 74.28
Residue 5: the 'mitochondrion outer membrane (mom)-targeting sequence' region

Full ARMCX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARMCX1 p.Ala127Val Uncertain significance ★ ⚠ same type
ARMCX1 p.Ala165Thr Uncertain significance ★ ⚠ same type
ARMCX1 p.Ala64Thr Uncertain significance ★ ⚠ same type
ARMCX1 p.Ala7Val Uncertain significance ★ ⚠ same type
ARMCX1 p.Arg216Gln Uncertain significance ★ ⚠ same type
ARMCX1 p.Arg299Cys Uncertain significance ★ ⚠ same type
ARMCX1 p.Arg299Gly Uncertain significance ★ ⚠ same type
ARMCX1 p.Arg31Lys 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/armcx1-p-arg5 (accessed [today's date]).

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