Is ABCC2 p.Phe977fs (c.2931_2995del) pathogenic?

ABCC2 p.Phe977fs (c.29312995del) is classified Pathogenic in ABCC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-24). Absent from gnomAD.

How common is ABCC2 p.Phe977fs (c.2931_2995del) in the general population?

ABCC2 p.Phe977fs (c.2931_2995del) is absent from gnomAD (gnomAD).

ABCC2 p.Phe977fs

c.2931_2995del · rs2493011457 · VCV2968556

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 22 of 32
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.28	GERP -2.5, phastCons 0.063

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: ABCC2
Protein: p.Phe977fs
Coding: c.2931_2995del
MANE Select: NM_000392
dbSNP: rs2493011457
Type: Deletion
Location: chr10:99831657 (GRCh38)
Gene constraint: LOEUF 0.985 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.40 · 16 PDB
Residue 977: an α-helix

Full ABCC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCC2 p.Asn159fs Pathogenic ★★ same type
ABCC2 p.Asn718fs Pathogenic/Likely pathogenic ★★ same type
ABCC2 p.Ile754fs Pathogenic ★★ same type
ABCC2 p.Leu431fs Pathogenic ★★ same type
ABCC2 p.Leu788fs Pathogenic/Likely pathogenic ★★ same type
ABCC2 p.Leu809fs Pathogenic/Likely pathogenic ★★ same type
ABCC2 p.Pro194_Ser195insTer Pathogenic ★★ same type
ABCC2 p.Pro274fs 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/abcc2-p-phe977fs (accessed [today's date]).

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