Is ABCC10 p.Arg804Gln (c.2411G>A) pathogenic?

ABCC10 p.Arg804Gln (c.2411G>A) is classified Likely benign in ABCC10 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-15). AlphaMissense: likely benign (0.0646); Very rare (popmax 0.00804%, afr).

How common is ABCC10 p.Arg804Gln (c.2411G>A) in the general population?

ABCC10 p.Arg804Gln (c.2411G>A) is very rare (popmax 0.00804%, afr) (gnomAD).

What do computational predictors say about ABCC10 p.Arg804Gln (c.2411G>A)?

AlphaMissense predicts likely benign (score 0.0646) — an in-silico prediction, not a clinical call.

ABCC10 p.Arg804Gln

c.2411G>A · rs767098942 · VCV2462053

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0646 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00804%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0646	likely benign
REVEL	0.25	benign-leaning
SaProt	LLR -7.40	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.27	gain · loss 0.17 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP -1.5	GERP -3.9
Regional constraint	o/e 0.89	unconstrained · MANE · 22 kb · p 4.2e-06 · regional, not allelic
Overall
CADD	0.953	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 0.00804% African / African-American · 6/74,612 alleles

Filtering AF 0.00348% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00239%

Overall 0.0032% 51/1,595,820 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00804%	12,435
European (non-Finnish)	0.00357%	28,002
Admixed American	0.00173%	57,968
Remaining individualsnot grpmax-eligible	0.00161%	61,920
South Asian	0.00112%	89,290

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.Arg804Gln
Coding: c.2411G>A
MANE Select: NM_001198934
dbSNP: rs767098942
Type: single nucleotide variant
Location: chr6:43443154 (GRCh38)
Gene constraint: LOEUF 0.894 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.32
Residue 804: the abc transporter 1 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-arg804gln (accessed [today's date]).

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