Is EFCAB6 p.Arg160= (c.480A>G) pathogenic?

EFCAB6 p.Arg160= (c.480A>G) is classified Likely benign in EFCAB6 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-01). Very rare (popmax 8.49e-05%, nfe).

How common is EFCAB6 p.Arg160= (c.480A>G) in the general population?

EFCAB6 p.Arg160= (c.480A>G) is very rare (popmax 8.49e-05%, nfe) (gnomAD).

EFCAB6 p.Arg160=

c.480A>G · rs767601462 · VCV2653270

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.49e-05%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.24	acceptor loss · deltas
Pangolin	Δ0.21	loss · gain 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP -0.47	GERP -2.1
Overall
CADD	3.166	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.49e-05% European (non-Finnish) · 1/1,178,156 alleles

Overall 6.22e-05% 1/1,607,452 alleles · very rare exomes 0/1,455,278 · genomes 1/152,174 · joint denominator

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: EFCAB6
Protein: p.Arg160=
Coding: c.480A>G
MANE Select: NM_022785
dbSNP: rs767601462
Type: single nucleotide variant
Location: chr22:43755793 (GRCh38)
Gene constraint: LOEUF 1.013 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.65 · 2 PDB

Full EFCAB6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EFCAB6 p.Ala1038Val Uncertain significance ★ ⚠ same type
EFCAB6 p.Ala1168Gly Uncertain significance ★ ⚠ same type
EFCAB6 p.Ala1203Val Uncertain significance ★ ⚠ same type
EFCAB6 p.Ala1296Glu Uncertain significance ★ ⚠ same type
EFCAB6 p.Ala1424Gly Uncertain significance ★ ⚠ same type
EFCAB6 p.Ala1457Val Uncertain significance ★ ⚠ same type
EFCAB6 p.Ala567Pro Uncertain significance ★ ⚠ same type
EFCAB6 p.Ala728Thr 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/efcab6-p-arg160 (accessed [today's date]).

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