Is ARPC4 c.3+17C>A pathogenic?

ARPC4 c.3+17C>A is classified Uncertain significance in ARPC4 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-14). Very rare (popmax 0.00239%, sas); Associated with Inborn genetic diseases.

What condition is associated with ARPC4 c.3+17C>A?

ARPC4 c.3+17C>A is associated with Inborn genetic diseases (ClinVar).

How common is ARPC4 c.3+17C>A in the general population?

ARPC4 c.3+17C>A is very rare (popmax 0.00239%, sas) (gnomAD).

ARPC4 c.3+17C>A

VCV4839267

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

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.084	moderately benign-leaning
Splicing
Splice region	donor +17	near-intronic (+17 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.86	GERP 0.19, phastCons 0.008
Non-coding constraint	Z -0.88	1 kb window · o/e 1.08 · regional · uncalibrated
Overall
CADD	7.573	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00239% South Asian · 2/83,748 alleles

Filtering AF 0.000396% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000218%

Overall 0.000792% 11/1,388,790 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00239%	41,874
Remaining individualsnot grpmax-eligible	0.00168%	59,696
European (non-Finnish)	0.000701%	142,745

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: ARPC4
Coding: c.3+17C>A
MANE Select: NM_005718
Type: single nucleotide variant
Location: chr3:9793141 (GRCh38)
Gene constraint: LOEUF 0.362 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 94.20 · 5 PDB

Full ARPC4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ARPC4 c.3+11C>G Uncertain significance ★ same condition
ARPC4 c.3+11C>T Uncertain significance ★ same condition
ARPC4 c.3+16C>T Uncertain significance ★ same condition
ARPC4 c.3+20G>A Uncertain significance ★ same condition
ARPC4 c.3+38G>A Uncertain significance ★ same condition
ARPC4 c.3+47C>T Uncertain significance ★ same condition
ARPC4 c.3+55T>G Uncertain significance ★ same condition
ARPC4 p.Arg32Gln 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/arpc4-c-3-plus-17c-a (accessed [today's date]).

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