Is ABCC10 p.Leu894= (c.2682C>G) pathogenic?

ABCC10 p.Leu894= (c.2682C>G) is classified Likely benign in ABCC10 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-01). Ultra-rare (popmax 0.0255%, afr).

How common is ABCC10 p.Leu894= (c.2682C>G) in the general population?

ABCC10 p.Leu894= (c.2682C>G) is ultra-rare (popmax 0.0255%, afr) (gnomAD).

ABCC10 p.Leu894=

c.2682C>G · rs773004616 · VCV2656600

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0255%, afr)

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 1.4	GERP -0.23, phastCons 1
Overall
CADD	7.16	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0255% African / African-American · 19/74,578 alleles

Filtering AF 0.0166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0138%

Overall 0.00118% 19/1,606,224 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: ABCC10
Protein: p.Leu894=
Coding: c.2682C>G
MANE Select: NM_001198934
dbSNP: rs773004616
Type: single nucleotide variant
Location: chr6:43444346 (GRCh38)
Gene constraint: LOEUF 0.894 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.32
Residue 894: the abc transmembrane type-1 2 domain

Full ABCC10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCC10 p.Met895Thr Uncertain significance ★★ ⚠ same type
ABCC10 p.Ala1050Ser Uncertain significance ★ ⚠ same type
ABCC10 p.Ala1119Thr Uncertain significance ★ ⚠ same type
ABCC10 p.Ala1165Thr Uncertain significance ★ ⚠ same type
ABCC10 p.Ala1179Thr Uncertain significance ★ ⚠ same type
ABCC10 p.Ala1324Pro Uncertain significance ★ ⚠ same type
ABCC10 p.Ala1324Ser Uncertain significance ★ ⚠ same type
ABCC10 p.Ala144Gly 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/abcc10-p-leu894 (accessed [today's date]).

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