Is SCO2 p.Asp173= (c.519C>T) pathogenic?

SCO2 p.Asp173= (c.519C>T) is classified Likely benign in SCO2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-09-28). Very rare (popmax 0.00619%, nfe).

How common is SCO2 p.Asp173= (c.519C>T) in the general population?

SCO2 p.Asp173= (c.519C>T) is very rare (popmax 0.00619%, nfe) (gnomAD).

SCO2 p.Asp173=

c.519C>T · rs145678414 · VCV2043049

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00619%, nfe)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -12	GERP -4.9
Overall
CADD	0.03	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00619% European (non-Finnish) · 73/1,180,006 alleles

Filtering AF 0.00503% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00462%

Overall 0.00471% 76/1,613,734 alleles · very rare exomes 72/1,461,532 · genomes 4/152,202 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00619%	16,164
East Asian	0.00223%	44,894
Remaining individualsnot grpmax-eligible	0.0016%	62,486
South Asian	0.0011%	91,090

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: SCO2
Protein: p.Asp173=
Coding: c.519C>T
MANE Select: NM_005138
dbSNP: rs145678414
Type: single nucleotide variant
Location: chr22:50523893 (GRCh38)

Full SCO2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/sco2-p-asp173 (accessed [today's date]).

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