Is B4GALNT1 p.Ala7= (c.21C>T) pathogenic?

B4GALNT1 p.Ala7= (c.21C>T) is classified Likely benign in B4GALNT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-12). Absent from gnomAD v4.1; Associated with Spastic paraplegia.

What condition is associated with B4GALNT1 p.Ala7= (c.21C>T)?

B4GALNT1 p.Ala7= (c.21C>T) is associated with Spastic paraplegia (ClinVar).

How common is B4GALNT1 p.Ala7= (c.21C>T) in the general population?

B4GALNT1 p.Ala7= (c.21C>T) is absent from gnomAD v4.1 (gnomAD).

B4GALNT1 p.Ala7=

c.21C>T · VCV4716609

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,500,136)

Conditions

Spastic paraplegia

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 1.3	GERP 1.7, phastCons 1
Overall
CADD	13.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,500,136). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: B4GALNT1
Protein: p.Ala7=
Coding: c.21C>T
MANE Select: NM_001478
Type: single nucleotide variant
Location: chr12:57632112 (GRCh38)
Gene constraint: LOEUF 1.114 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.79 · 3 PDB

Full B4GALNT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Spastic paraplegia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

B4GALNT1 p.Ala7Thr Uncertain significance ★★ ⚠ same residue
B4GALNT1 c.383+1G>A Likely pathogenic ★★ same condition
B4GALNT1 c.490+1G>A Pathogenic/Likely pathogenic ★★ same condition
B4GALNT1 c.532-2A>G Pathogenic/Likely pathogenic ★★ same condition
B4GALNT1 p.Ala393Val Uncertain significance ★★ ⚠ same condition
B4GALNT1 p.Arg300His Uncertain significance ★★ ⚠ same condition
B4GALNT1 p.Arg397Trp Uncertain significance ★★ ⚠ same condition
B4GALNT1 p.Asp511Glu Uncertain significance ★★ ⚠ same condition

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/b4galnt1-p-ala7 (accessed [today's date]).

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