Is ABCB7 p.Val401= (c.1203G>A) pathogenic?

ABCB7 p.Val401= (c.1203G>A) is classified Benign/Likely benign in ABCB7 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-24). Ultra-rare (popmax 0.0175%, amr).

How common is ABCB7 p.Val401= (c.1203G>A) in the general population?

ABCB7 p.Val401= (c.1203G>A) is ultra-rare (popmax 0.0175%, amr) (gnomAD).

ABCB7 p.Val401=

c.1203G>A · rs763867013 · VCV506643

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0175%, amr)

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 0.54	GERP 0.74, phastCons 1
Overall
CADD	6.936	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0175% Admixed American · 8/45,607 alleles

Filtering AF 0.00871% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00632%

Overall 0.000662% 8/1,208,893 alleles · ultra-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.Val401=
Coding: c.1203G>A
MANE Select: NM_001271696
dbSNP: rs763867013
Type: single nucleotide variant
Location: chrX:75071513 (GRCh38)
Structure: AlphaFold pLDDT 78.19 · 4 PDB
Residue 401: 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 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
ABCB7 p.Glu494Gln Uncertain significance ★★ ⚠ same type
ABCB7 p.Gly197Cys 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-val401 (accessed [today's date]).

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