Is CSGALNACT1 p.Phe327= (c.981C>T) pathogenic?

CSGALNACT1 p.Phe327= (c.981C>T) is classified Likely benign in CSGALNACT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-05). Absent from gnomAD v4.1.

How common is CSGALNACT1 p.Phe327= (c.981C>T) in the general population?

CSGALNACT1 p.Phe327= (c.981C>T) is absent from gnomAD v4.1 (gnomAD).

CSGALNACT1 p.Phe327=

c.981C>T · rs2538097935 · VCV3015756

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 4.4	GERP -0.65, phastCons 1
Overall
CADD	11.52	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CSGALNACT1
Protein: p.Phe327=
Coding: c.981C>T
MANE Select: NM_001354483
dbSNP: rs2538097935
Type: single nucleotide variant
Location: chr8:19420491 (GRCh38)
Gene constraint: LOEUF 1.257 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.71

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

Similar variants

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
CSGALNACT1 p.Arg202His 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-phe327 (accessed [today's date]).

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