Is SI p.Arg963= (c.2887A>C) pathogenic?

SI p.Arg963= (c.2887A>C) is classified Benign/Likely benign in SI (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-02). Low-frequency (popmax 1.84%, afr); Associated with congenital sucrase-isomaltase deficiency.

What condition is associated with SI p.Arg963= (c.2887A>C)?

SI p.Arg963= (c.2887A>C) is associated with congenital sucrase-isomaltase deficiency (ClinVar).

How common is SI p.Arg963= (c.2887A>C) in the general population?

SI p.Arg963= (c.2887A>C) is low-frequency (popmax 1.84%, afr) (gnomAD).

How is Congenital sucrase-isomaltase deficiency inherited?

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

SI p.Arg963=

c.2887A>C · rs113456182 · VCV344036

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.84%, afr)

Conditions

congenital sucrase-isomaltase deficiency

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 -8.7	GERP -3.2
Overall
CADD	0.053	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.84% African / African-American · 1,374/74,558 alleles

Filtering AF 1.76% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.73%

Overall 0.0973% 1,565/1,608,216 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.84%	54
Remaining individualsnot grpmax-eligible	0.162%	616
Admixed American	0.0974%	1,027
Middle Eastern	0.034%	2,941
East Asian	0.0134%	7,443
South Asian	0.00991%	10,095
European (non-Finnish)	0.00128%	78,417

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: SI
Protein: p.Arg963=
Coding: c.2887A>C
MANE Select: NM_001041
dbSNP: rs113456182
Type: single nucleotide variant
Location: chr3:165030717 (GRCh38)
Gene constraint: LOEUF 1.009 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.86 · 2 PDB
Residue 963: the 'isomaltase' region; the p-type 2 domain

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

Disease context

congenital sucrase-isomaltase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital sucrase-isomaltase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

SI p.Arg963Lys Likely benign ★★ same residue
SI c.2426+1G>A Likely pathogenic ★★ same condition
SI c.2893-1G>A Likely pathogenic ★★ same condition
SI c.3099+1G>C Likely pathogenic ★★ same condition
SI c.3521-1G>T Likely pathogenic ★★ same condition
SI c.373+1G>A Likely pathogenic ★★ same condition
SI c.4575+2T>C Likely pathogenic ★★ same condition
SI c.4927-1G>A Likely pathogenic ★★ 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/si-p-arg963 (accessed [today's date]).

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