Is SI p.Arg1484His (c.4451G>A) pathogenic?

SI p.Arg1484His (c.4451G>A) is classified Uncertain significance in SI (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-06-05). AlphaMissense: likely pathogenic (0.8968); Ultra-rare (popmax 0.0609%, nfe); Associated with congenital sucrase-isomaltase deficiency.

What condition is associated with SI p.Arg1484His (c.4451G>A)?

SI p.Arg1484His (c.4451G>A) is associated with congenital sucrase-isomaltase deficiency (ClinVar).

How common is SI p.Arg1484His (c.4451G>A) in the general population?

SI p.Arg1484His (c.4451G>A) is ultra-rare (popmax 0.0609%, nfe) (gnomAD).

How is Congenital sucrase-isomaltase deficiency inherited?

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

What do computational predictors say about SI p.Arg1484His (c.4451G>A)?

AlphaMissense predicts likely pathogenic (score 0.8968) — an in-silico prediction, not a clinical call.

SI p.Arg1484His

c.4451G>A · rs145246112 · VCV1504591

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely pathogenic

0.8968 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0609%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

congenital sucrase-isomaltase deficiency

Computational evidence

Protein change
AlphaMissense	0.8968	likely pathogenic
REVEL	0.954	strongly pathogenic-leaning
SaProt	LLR -12.45	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.31 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.5	GERP 1.8, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 97 kb · p 9.1e-07 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0609% European (non-Finnish) · 717/1,177,976 alleles

Filtering AF 0.0571% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0557%

Overall 0.0482% 776/1,611,284 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0609%	1,643
Remaining individualsnot grpmax-eligible	0.0257%	3,898
Admixed American	0.0201%	4,980
Finnishnot grpmax-eligible	0.0125%	7,999
South Asian	0.0121%	8,277
African / African-American	0.012%	8,320
East Asian	0.0067%	14,929

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.Arg1484His
Coding: c.4451G>A
MANE Select: NM_001041
dbSNP: rs145246112
Type: single nucleotide variant
Location: chr3:164998629 (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 1484: the 'sucrase' region

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.Arg1484Cys Uncertain significance ★ ⚠ 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-arg1484his (accessed [today's date]).

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