Is ABCB7 p.Arg313Gln (c.938G>A) pathogenic?

ABCB7 p.Arg313Gln (c.938G>A) is classified Benign/Likely benign in ABCB7 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-01-20). AlphaMissense: likely benign (0.0604); Rare (popmax 0.448%, nfe); Associated with X-linked sideroblastic anemia with ataxia.

What condition is associated with ABCB7 p.Arg313Gln (c.938G>A)?

ABCB7 p.Arg313Gln (c.938G>A) is associated with X-linked sideroblastic anemia with ataxia (ClinVar).

How common is ABCB7 p.Arg313Gln (c.938G>A) in the general population?

ABCB7 p.Arg313Gln (c.938G>A) is rare (popmax 0.448%, nfe) (gnomAD).

What do computational predictors say about ABCB7 p.Arg313Gln (c.938G>A)?

AlphaMissense predicts likely benign (score 0.0604) — an in-silico prediction, not a clinical call.

ABCB7 p.Arg313Gln

Q: How is X-linked sideroblastic anemia and spinocerebellar ataxia inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.938G>A · rs147584361 · VCV136243

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

AlphaMissense

likely benign

0.0604 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.448%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

X-linked sideroblastic anemia with ataxia

Computational evidence

Protein change
AlphaMissense	0.0604	likely benign
REVEL	0.222	benign-leaning
SaProt	LLR -2.73	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 1.4, phastCons 1
Regional constraint	o/e 0.51	unconstrained · MANE · 46 kb · p 3.2e-26 · regional, not allelic
Overall
CADD	18.85	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 0.448% European (non-Finnish) · 3,994/892,512 alleles

Filtering AF 0.436% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.431%

Overall 0.363% 4,386/1,207,153 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.448%	223
Ashkenazi Jewishnot grpmax-eligible	0.282%	355
Remaining individualsnot grpmax-eligible	0.278%	360
Admixed American	0.151%	663
Middle Eastern	0.115%	870
Finnishnot grpmax-eligible	0.0923%	1,083
African / African-American	0.0786%	1,272
South Asian	0.0634%	1,578

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.Arg313Gln
Coding: c.938G>A
MANE Select: NM_001271696
dbSNP: rs147584361
Type: single nucleotide variant
Location: chrX:75073874 (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

Disease context

X-linked sideroblastic anemia with ataxia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked sideroblastic anemia and spinocerebellar ataxia (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood, Infancy

Similar variants

ABCB7 p.Arg313Trp Uncertain significance ★ ⚠ same residue
ABCB7 p.Arg313= Likely benign ★ same residue
ABCB7 c.1935+5G>C Uncertain significance ★★ same condition
ABCB7 c.1032+12A>G Benign/Likely benign ★★ same condition
ABCB7 c.168+69C>G Benign ★★ same condition
ABCB7 c.945-7C>T Benign/Likely benign ★★ same condition
ABCB7 p.Ala580Val Benign/Likely benign ★★ ⚠ same condition
ABCB7 p.Gln67His Benign/Likely benign ★★ 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-arg313gln (accessed [today's date]).

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