Is ABCC1 p.Arg633Gln (c.1898G>A) pathogenic?

ABCC1 p.Arg633Gln (c.1898G>A) is classified Likely benign in ABCC1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-10-19). AlphaMissense: likely benign (0.0685); Rare (popmax 0.372%, nfe); Associated with ABCC1-related disorder.

What condition is associated with ABCC1 p.Arg633Gln (c.1898G>A)?

ABCC1 p.Arg633Gln (c.1898G>A) is associated with ABCC1-related disorder (ClinVar).

How common is ABCC1 p.Arg633Gln (c.1898G>A) in the general population?

ABCC1 p.Arg633Gln (c.1898G>A) is rare (popmax 0.372%, nfe) (gnomAD).

What do computational predictors say about ABCC1 p.Arg633Gln (c.1898G>A)?

AlphaMissense predicts likely benign (score 0.0685) — an in-silico prediction, not a clinical call.

ABCC1 p.Arg633Gln

c.1898G>A · rs112282109 · VCV3041981

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0685 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.372%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ABCC1-related disorder

Computational evidence

Protein change
AlphaMissense	0.0685	likely benign
REVEL	0.015	strongly benign-leaning
SaProt	LLR -5.37	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 0.046	GERP -2.5
Regional constraint	o/e 0.88	unconstrained · MANE · 97 kb · p 2.5e-06 · regional, not allelic
Overall
CADD	9.29	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 0.372% European (non-Finnish) · 4,393/1,179,806 alleles

Filtering AF 0.363% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.359%

Overall 0.295% 4,759/1,613,638 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.372%	269
Remaining individualsnot grpmax-eligible	0.256%	390
Ashkenazi Jewishnot grpmax-eligible	0.155%	643
Middle Eastern	0.099%	1,010
Admixed American	0.0917%	1,090
African / African-American	0.0773%	1,294
Finnishnot grpmax-eligible	0.0516%	1,940
South Asian	0.0088%	11,363

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: ABCC1
Protein: p.Arg633Gln
Coding: c.1898G>A
MANE Select: NM_004996
dbSNP: rs112282109
Type: single nucleotide variant
Location: chr16:16071715 (GRCh38)
Gene constraint: LOEUF 0.564 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.01 · 5 PDB
Residue 633: a UniProt-annotated variant site (in)

Full ABCC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ABCC1-related disorder

Similar variants

ABCC1 p.Arg62Gln Benign ⚠ same condition
ABCC1 p.Asn412Ser Likely benign same condition
ABCC1 p.Gly639Trp Likely benign ⚠ same condition
ABCC1 p.Pro285Leu Likely benign same condition
ABCC1 p.Ser92Phe Benign ⚠ same condition
ABCC1 p.Thr1401Met Likely benign ⚠ same condition
ABCC1 p.Val1481Ile Benign ⚠ same condition
ABCC1 p.Thr1464Met 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/abcc1-p-arg633gln (accessed [today's date]).

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