Is CSGALNACT1 p.Pro384= (c.1152A>T) pathogenic?

CSGALNACT1 p.Pro384= (c.1152A>T) is classified Likely benign in CSGALNACT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-18). Very rare (popmax 0.00212%, nfe).

How common is CSGALNACT1 p.Pro384= (c.1152A>T) in the general population?

CSGALNACT1 p.Pro384= (c.1152A>T) is very rare (popmax 0.00212%, nfe) (gnomAD).

CSGALNACT1 p.Pro384=

c.1152A>T · VCV3628382

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00212%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.21	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -9.6	GERP -4.7
Overall
CADD	1.533	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00212% European (non-Finnish) · 25/1,177,636 alleles

Filtering AF 0.00146% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00123%

Overall 0.00155% 25/1,611,462 alleles · very rare exomes 23/1,459,246 · genomes 2/152,216 · 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: CSGALNACT1
Protein: p.Pro384=
Coding: c.1152A>T
MANE Select: NM_001354483
Type: single nucleotide variant
Location: chr8:19418731 (GRCh38)
Gene constraint: LOEUF 1.257 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.71
Residue 384: a UniProt-annotated variant site (in sdjlaba; loss of galnac-transferase activity)

Full CSGALNACT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSGALNACT1 p.Pro384Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
CSGALNACT1 p.Asn264Ser Likely pathogenic ★★ ⚠ same type
CSGALNACT1 c.634+5G>C Uncertain significance ★★ same type
CSGALNACT1 p.Ala195Ser Uncertain significance ★★ ⚠ same type
CSGALNACT1 p.Ala259Gly Uncertain significance ★★ ⚠ same type
CSGALNACT1 p.Ala401Ser Uncertain significance ★★ ⚠ same type
CSGALNACT1 p.Ala48Gly Uncertain significance ★★ ⚠ same type
CSGALNACT1 p.Arg202Cys 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/csgalnact1-p-pro384 (accessed [today's date]).

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