Is SI p.Asp1413= (c.4239C>T) pathogenic?

SI p.Asp1413= (c.4239C>T) is classified Conflicting classifications of pathogenicity in SI (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-11-25). Rare (popmax 0.157%, sas); Associated with congenital sucrase-isomaltase deficiency.

What condition is associated with SI p.Asp1413= (c.4239C>T)?

SI p.Asp1413= (c.4239C>T) is associated with congenital sucrase-isomaltase deficiency (ClinVar).

How common is SI p.Asp1413= (c.4239C>T) in the general population?

SI p.Asp1413= (c.4239C>T) is rare (popmax 0.157%, sas) (gnomAD).

How is Congenital sucrase-isomaltase deficiency inherited?

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

SI p.Asp1413=

c.4239C>T · rs138374817 · VCV344013

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.157%, sas)

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 -5.8	GERP -3.2
Overall
CADD	0.451	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.157% South Asian · 142/90,584 alleles

Filtering AF 0.136% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.128%

Overall 0.0227% 363/1,597,504 alleles · rare exomes 330/1,446,532 · genomes 33/150,972 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.157%	638
Middle Eastern	0.0499%	2,004
Remaining individualsnot grpmax-eligible	0.0242%	4,126
African / African-American	0.0202%	4,962
European (non-Finnish)	0.0149%	6,705
Finnishnot grpmax-eligible	0.0126%	7,921
Admixed American	0.00669%	14,938
Ashkenazi Jewishnot grpmax-eligible	0.0034%	29,382
East Asian	0.00225%	44,430

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.Asp1413=
Coding: c.4239C>T
MANE Select: NM_001041
dbSNP: rs138374817
Type: single nucleotide variant
Location: chr3:165007939 (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 1413: 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 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
SI c.5248-2A>C 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-asp1413 (accessed [today's date]).

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