Is ABCC6 p.Arg473fs (c.1413del) pathogenic?

ABCC6 p.Arg473fs (c.1413del) is classified Pathogenic/Likely pathogenic in ABCC6 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-11-28). Absent from gnomAD; Associated with ABCC6-related disorder.

What condition is associated with ABCC6 p.Arg473fs (c.1413del)?

ABCC6 p.Arg473fs (c.1413del) is associated with ABCC6-related disorder, autosomal recessive inherited pseudoxanthoma elasticum (ClinVar).

How common is ABCC6 p.Arg473fs (c.1413del) in the general population?

ABCC6 p.Arg473fs (c.1413del) is absent from gnomAD (gnomAD).

ABCC6 p.Arg473fs

c.1413del · rs1596687174 · VCV812212

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ABCC6-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 11 of 31
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 1.4, phastCons 1

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: ABCC6
Protein: p.Arg473fs
Coding: c.1413del
MANE Select: NM_001171
dbSNP: rs1596687174
Type: Deletion
Location: chr16:16192848 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.32 · 4 PDB
Residue 473: the abc transmembrane type-1 1 domain

Full ABCC6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ABCC6-related disorder

Also linked: autosomal recessive inherited pseudoxanthoma elasticum

Similar variants

ABCC6 c.2248-2_2248-1del Pathogenic ★★ same condition
ABCC6 c.3506+2_3506+5del Pathogenic/Likely pathogenic ★★ same condition
ABCC6 c.998+2_998+3del Pathogenic/Likely pathogenic ★★ same condition
ABCC6 p.Ala667fs Pathogenic/Likely pathogenic ★★ same condition
ABCC6 p.Asp1368fs Pathogenic ★★ same condition
ABCC6 p.Glu559fs Pathogenic/Likely pathogenic ★★ same condition
ABCC6 p.Leu775fs Likely pathogenic ★★ same condition
ABCC6 p.Leu780fs Pathogenic/Likely pathogenic ★★ 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/abcc6-p-arg473fs (accessed [today's date]).

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