Is ABCB7 p.Gly682Ser (c.2044G>A) pathogenic?

ABCB7 p.Gly682Ser (c.2044G>A) is classified Likely pathogenic in ABCB7 (ClinVar, Single submitter, 2 submitters; last evaluated 2016-01-15). AlphaMissense: likely pathogenic (0.7444); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ABCB7 p.Gly682Ser (c.2044G>A)?

ABCB7 p.Gly682Ser (c.2044G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ABCB7 p.Gly682Ser (c.2044G>A) in the general population?

ABCB7 p.Gly682Ser (c.2044G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABCB7 p.Gly682Ser (c.2044G>A)?

AlphaMissense predicts likely pathogenic (score 0.7444) — an in-silico prediction, not a clinical call.

ABCB7 p.Gly682Ser

c.2044G>A · rs797044558 · VCV208533

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.7444 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.7444	likely pathogenic ✓ concordant with ClinVar
REVEL	0.957	strongly pathogenic-leaning
SaProt	LLR -14.73	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	Δ0.26	acceptor loss · deltas
Pangolin	Δ0.34	loss · gain 0.02 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 7.6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.51	unconstrained · MANE · 46 kb · p 3.2e-26 · regional, not allelic
Overall
CADD	32.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ABCB7
Protein: p.Gly682Ser
Coding: c.2044G>A
MANE Select: NM_001271696
dbSNP: rs797044558
Type: single nucleotide variant
Location: chrX:75053585 (GRCh38)
Structure: AlphaFold pLDDT 78.19 · 4 PDB
Residue 682: the abc transporter domain

Full ABCB7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCB7 p.Ala5Glu Uncertain significance ★★ ⚠ same condition
ABCB7 p.Asp653Asn Uncertain significance ★★ ⚠ same condition
ABCB7 p.Leu272Phe Uncertain significance ★★ ⚠ same condition
ABCB7 p.Leu395Val Uncertain significance ★★ ⚠ same condition
ABCB7 p.Met175Val Uncertain significance ★★ ⚠ same condition
ABCB7 p.Met441Val Uncertain significance ★★ ⚠ same condition
ABCB7 p.Ser641Leu Uncertain significance ★★ ⚠ same condition
ABCB7 p.Thr187Ala Uncertain significance ★★ ⚠ 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/abcb7-p-gly682ser (accessed [today's date]).

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