Is SQOR p.Val7= (c.21G>A) pathogenic?

SQOR p.Val7= (c.21G>A) is classified Likely benign in SQOR (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-06-10). Rare (popmax 0.308%, afr); Associated with SQOR-related disorder.

What condition is associated with SQOR p.Val7= (c.21G>A)?

SQOR p.Val7= (c.21G>A) is associated with SQOR-related disorder (ClinVar).

How common is SQOR p.Val7= (c.21G>A) in the general population?

SQOR p.Val7= (c.21G>A) is rare (popmax 0.308%, afr) (gnomAD).

SQOR p.Val7=

c.21G>A · VCV3357531

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.308%, afr)

Conditions

SQOR-related disorder

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 6.2	GERP 1.6, phastCons 1
Overall
CADD	4.715	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.308% African / African-American · 228/74,100 alleles

Filtering AF 0.275% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.262%

Overall 0.0165% 259/1,570,246 alleles · rare exomes 135/1,417,930 · genomes 124/152,316 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.308%	325
Admixed American	0.0196%	5,099
Remaining individualsnot grpmax-eligible	0.0183%	5,477
East Asian	0.016%	6,237
South Asian	0.00115%	86,844
European (non-Finnish)	8.67e-05%	1,153,160

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.Val7=
Coding: c.21G>A
MANE Select: NM_021199
Type: single nucleotide variant
Location: chr15:45658944 (GRCh38)
Gene constraint: LOEUF 0.972 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.42 · 8 PDB

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

Disease context

SQOR-related disorder

Similar variants

SQOR p.Val318Met Likely benign same condition
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

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-val7 (accessed [today's date]).

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