Is ABCF2 p.Val511Met (c.1531G>A) pathogenic?

ABCF2 p.Val511Met (c.1531G>A) is classified Uncertain significance in ABCF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-28). AlphaMissense: likely pathogenic (0.6002); Very rare (popmax 0.0011%, nfe).

How common is ABCF2 p.Val511Met (c.1531G>A) in the general population?

ABCF2 p.Val511Met (c.1531G>A) is very rare (popmax 0.0011%, nfe) (gnomAD).

What do computational predictors say about ABCF2 p.Val511Met (c.1531G>A)?

AlphaMissense predicts likely pathogenic (score 0.6002) — an in-silico prediction, not a clinical call.

ABCF2 p.Val511Met

c.1531G>A · VCV3410838

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6002 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0011%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6002	likely pathogenic
REVEL	0.482	indeterminate
SaProt	LLR -8.46	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.38 · evaluated, not missing
Pangolin	Δ0.43	loss · gain 0.33 · SpliceAI below 0.2 · independent
Constraint at this position
Conservation	phyloP 7.6	GERP 1.5, phastCons 1
Regional constraint	o/e 0.56	unconstrained · MANE · 4,809 bp · p 1.3e-16 · regional, not allelic
Overall
CADD	25.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% European (non-Finnish) · 13/1,179,204 alleles

Filtering AF 0.000615% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000474%

Overall 0.00089% 13/1,460,112 alleles · very rare

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: ABCF2
Protein: p.Val511Met
Coding: c.1531G>A
MANE Select: NM_007189
Type: single nucleotide variant
Location: chr7:151215082 (GRCh38)
Gene constraint: LOEUF 0.61 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.57
Residue 511: the abc transporter 2 domain

Full ABCF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCF2 p.Arg113His Uncertain significance ★ ⚠ same type
ABCF2 p.Arg223His Uncertain significance ★ ⚠ same type
ABCF2 p.Asp166Asn Uncertain significance ★ ⚠ same type
ABCF2 p.Asp202Asn Uncertain significance ★ ⚠ same type
ABCF2 p.Asp519Asn Uncertain significance ★ ⚠ same type
ABCF2 p.Gln399His Uncertain significance ★ ⚠ same type
ABCF2 p.Glu373Asp Uncertain significance ★ ⚠ same type
ABCF2 p.Glu550Lys 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/abcf2-p-val511met (accessed [today's date]).

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