Is B4GALNT4 p.Ser857= (c.2571C>T) pathogenic?

B4GALNT4 p.Ser857= (c.2571C>T) is classified Likely benign in B4GALNT4 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-01). Rare (popmax 0.693%, mid).

How common is B4GALNT4 p.Ser857= (c.2571C>T) in the general population?

B4GALNT4 p.Ser857= (c.2571C>T) is rare (popmax 0.693%, mid) (gnomAD).

B4GALNT4 p.Ser857=

c.2571C>T · rs142922840 · VCV2641041

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.693%, mid)

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 -0.32	GERP -3.2, phastCons 0.005
Overall
CADD	10.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.693% Middle Eastern · 42/6,060 alleles

Filtering AF 0.527% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.469%

Overall 0.262% 4,227/1,612,298 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.81%	55
Middle Easterngrpmax	0.693%	144
Remaining individualsnot grpmax-eligible	0.307%	325
European (non-Finnish)	0.264%	379
Admixed American	0.217%	462
South Asian	0.195%	512
African / African-American	0.0413%	2,421
Finnishnot grpmax-eligible	0.016%	6,243

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: B4GALNT4
Protein: p.Ser857=
Coding: c.2571C>T
MANE Select: NM_178537
dbSNP: rs142922840
Type: single nucleotide variant
Location: chr11:379948 (GRCh38)
Gene constraint: LOEUF 1.059 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.89

Full B4GALNT4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

B4GALNT4 p.Asn430Ser Benign ★★ same type
B4GALNT4 p.Pro160= Benign ★★ same type
B4GALNT4 p.Ala133Thr Uncertain significance ★ ⚠ same type
B4GALNT4 p.Ala204Ser Uncertain significance ★ ⚠ same type
B4GALNT4 p.Ala208Gly Uncertain significance ★ ⚠ same type
B4GALNT4 p.Ala219Val Uncertain significance ★ ⚠ same type
B4GALNT4 p.Ala294Val Uncertain significance ★ ⚠ same type
B4GALNT4 p.Ala345Val 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/b4galnt4-p-ser857 (accessed [today's date]).

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