Is PUS3 p.Asp337= (c.1011C>T) pathogenic?

PUS3 p.Asp337= (c.1011C>T) is classified Benign/Likely benign in PUS3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-05). Rare (popmax 0.992%, sas).

How common is PUS3 p.Asp337= (c.1011C>T) in the general population?

PUS3 p.Asp337= (c.1011C>T) is rare (popmax 0.992%, sas) (gnomAD).

PUS3 p.Asp337=

c.1011C>T · rs200292412 · VCV741920

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.992%, sas)

⚠ 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 2.7	GERP -0.12, phastCons 1
Overall
CADD	5.568	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.992% South Asian · 903/91,048 alleles

Filtering AF 0.938% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.917%

Overall 0.0604% 974/1,613,194 alleles · rare exomes 912/1,461,026 · genomes 62/152,168 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.992%	101
Remaining individualsnot grpmax-eligible	0.0656%	1,524
Middle Eastern	0.033%	3,030
East Asian	0.00446%	22,439
African / African-American	0.004%	24,993
European (non-Finnish)	0.00195%	51,273

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: PUS3
Protein: p.Asp337=
Coding: c.1011C>T
MANE Select: NM_031307
dbSNP: rs200292412
Type: single nucleotide variant
Location: chr11:125894220 (GRCh38)

Full PUS3 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/pus3-p-asp337 (accessed [today's date]).

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