Is ABCC6 p.Phe586fs (c.1755del) pathogenic?

ABCC6 p.Phe586fs (c.1755del) is classified Pathogenic in ABCC6 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-05). Absent from gnomAD.

How common is ABCC6 p.Phe586fs (c.1755del) in the general population?

ABCC6 p.Phe586fs (c.1755del) is absent from gnomAD (gnomAD).

ABCC6 p.Phe586fs

c.1755del · rs2047742790 · VCV2764901

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 13 of 31
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.8	GERP -0.53, 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.Phe586fs
Coding: c.1755del
MANE Select: NM_001171
dbSNP: rs2047742790
Type: Deletion
Location: chr16:16188855 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.32 · 4 PDB
Residue 586: the abc transmembrane type-1 1 domain

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

Similar variants

ABCC6 c.2248-2_2248-1del Pathogenic ★★ same type
ABCC6 c.3506+2_3506+5del Pathogenic/Likely pathogenic ★★ same type
ABCC6 c.998+2_998+3del Pathogenic/Likely pathogenic ★★ same type
ABCC6 p.Ala667fs Pathogenic/Likely pathogenic ★★ same type
ABCC6 p.Arg473fs Pathogenic/Likely pathogenic ★★ same type
ABCC6 p.Asp1368fs Pathogenic ★★ same type
ABCC6 p.Glu559fs Pathogenic/Likely pathogenic ★★ same type
ABCC6 p.Leu430fs Pathogenic/Likely pathogenic ★★ 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/abcc6-p-phe586fs (accessed [today's date]).

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