Is ABCB7 p.Arg313= (c.939G>A) pathogenic?

ABCB7 p.Arg313= (c.939G>A) is classified Likely benign in ABCB7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-03). Very rare (popmax 9.13e-05%).

How common is ABCB7 p.Arg313= (c.939G>A) in the general population?

ABCB7 p.Arg313= (c.939G>A) is very rare (popmax 9.13e-05%) (gnomAD).

ABCB7 p.Arg313=

c.939G>A · VCV4765895

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 9.13e-05%)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.24	GERP -0.28, phastCons 0.23
Overall
CADD	7.958	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 9.13e-05%

Overall 9.13e-05% 1/1,095,151 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: ABCB7
Protein: p.Arg313=
Coding: c.939G>A
MANE Select: NM_001271696
Type: single nucleotide variant
Location: chrX:75073873 (GRCh38)
Structure: AlphaFold pLDDT 78.19 · 4 PDB
Residue 313: the abc transmembrane type-1 domain; an α-helix

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

Similar variants

ABCB7 p.Arg313Gln Benign/Likely benign ★★ same residue
ABCB7 p.Arg313Trp Uncertain significance ★ ⚠ same residue
ABCB7 c.1659+5T>G Uncertain significance ★★ same type
ABCB7 c.1935+5G>C Uncertain significance ★★ same type
ABCB7 p.Ala5Glu Uncertain significance ★★ ⚠ same type
ABCB7 p.Arg711His Uncertain significance ★★ ⚠ same type
ABCB7 p.Asn378Asp Uncertain significance ★★ ⚠ same type
ABCB7 p.Asp653Asn 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/abcb7-p-arg313 (accessed [today's date]).

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