Is SQOR p.Pro300Ser (c.898C>T) pathogenic?

SQOR p.Pro300Ser (c.898C>T) is classified Likely benign in SQOR (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-26). AlphaMissense: likely benign (0.1187); Very rare (popmax 0.000339%, nfe).

How common is SQOR p.Pro300Ser (c.898C>T) in the general population?

SQOR p.Pro300Ser (c.898C>T) is very rare (popmax 0.000339%, nfe) (gnomAD).

What do computational predictors say about SQOR p.Pro300Ser (c.898C>T)?

AlphaMissense predicts likely benign (score 0.1187) — an in-silico prediction, not a clinical call.

SQOR p.Pro300Ser

c.898C>T · VCV3961807

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1187 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1187	likely benign
REVEL	0.144	moderately benign-leaning
SaProt	LLR -6.91	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 -2
Regional constraint	o/e 1.00	unconstrained · MANE · 32 kb · p 0.96 · regional, not allelic
Overall
CADD	3.42	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 0.000339% European (non-Finnish) · 4/1,180,034 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000248% 4/1,614,152 alleles · very rare exomes 4/1,461,862 · genomes 0/152,290 · joint denominator

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: SQOR
Protein: p.Pro300Ser
Coding: c.898C>T
MANE Select: NM_021199
Type: single nucleotide variant
Location: chr15:45682511 (GRCh38)
Gene constraint: LOEUF 0.972 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.42 · 8 PDB
Residue 300: a β-strand

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

Similar variants

SQOR p.Arg61His Uncertain significance ★★ ⚠ same type
SQOR p.Ala144Thr Uncertain significance ★ ⚠ same type
SQOR p.Ala162Thr Uncertain significance ★ ⚠ same type
SQOR p.Ala17Asp Uncertain significance ★ ⚠ same type
SQOR p.Ala346Val Uncertain significance ★ ⚠ same type
SQOR p.Ala39Val Uncertain significance ★ ⚠ same type
SQOR p.Ala72Val Uncertain significance ★ ⚠ same type
SQOR p.Arg101Cys 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/sqor-p-pro300ser (accessed [today's date]).

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