Is SI p.Pro331Ser (c.991C>T) pathogenic?

SI p.Pro331Ser (c.991C>T) is classified Uncertain significance in SI (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-04). AlphaMissense: likely pathogenic (0.787); Very rare (popmax 0.00502%, amr); Associated with Inborn genetic diseases.

What condition is associated with SI p.Pro331Ser (c.991C>T)?

SI p.Pro331Ser (c.991C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SI p.Pro331Ser (c.991C>T) in the general population?

SI p.Pro331Ser (c.991C>T) is very rare (popmax 0.00502%, amr) (gnomAD).

What do computational predictors say about SI p.Pro331Ser (c.991C>T)?

AlphaMissense predicts likely pathogenic (score 0.787) — an in-silico prediction, not a clinical call.

SI p.Pro331Ser

c.991C>T · rs201980143 · VCV2515691

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.787 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00502%, amr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.787	likely pathogenic
REVEL	0.89	moderately pathogenic-leaning
SaProt	LLR -9.49	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 12	GERP 1.6, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 97 kb · p 9.1e-07 · regional, not allelic
Overall
CADD	27.1	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 0.00502% Admixed American · 3/59,804 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000845%

Overall 0.00157% 25/1,589,494 alleles · very rare exomes 21/1,437,462 · genomes 4/152,032 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00502%	19,935
African / African-American	0.00269%	37,217
European (non-Finnish)	0.00164%	60,962
Remaining individualsnot grpmax-eligible	0.00162%	61,592

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.Pro331Ser
Coding: c.991C>T
MANE Select: NM_001041
dbSNP: rs201980143
Type: single nucleotide variant
Location: chr3:165062400 (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 331: the 'isomaltase' region; an α-helix

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SI p.Ala1654Asp Uncertain significance ★★ ⚠ same condition
SI p.Ala429Thr Uncertain significance ★★ ⚠ same condition
SI p.Ala573Val Uncertain significance ★★ ⚠ same condition
SI p.Ala760Val Uncertain significance ★★ ⚠ same condition
SI p.Ala808Thr Uncertain significance ★★ ⚠ same condition
SI p.Ala826Asp Uncertain significance ★★ ⚠ same condition
SI p.Arg1078Gln Uncertain significance ★★ same condition
SI p.Arg1078Trp Uncertain significance ★★ ⚠ 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-pro331ser (accessed [today's date]).

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