Is B4GALT7 p.Pro80= (c.240C>T) pathogenic?

B4GALT7 p.Pro80= (c.240C>T) is classified Likely benign in B4GALT7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-26). Very rare (popmax 0.00267%, afr); Associated with Ehlers-Danlos syndrome, spondylodysplastic type.

What condition is associated with B4GALT7 p.Pro80= (c.240C>T)?

B4GALT7 p.Pro80= (c.240C>T) is associated with Ehlers-Danlos syndrome, spondylodysplastic type (ClinVar).

How common is B4GALT7 p.Pro80= (c.240C>T) in the general population?

B4GALT7 p.Pro80= (c.240C>T) is very rare (popmax 0.00267%, afr) (gnomAD).

B4GALT7 p.Pro80=

c.240C>T · rs377379133 · VCV1582504

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

Ehlers-Danlos syndrome, spondylodysplastic type

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 -2.9	GERP -2.3
Overall
CADD	6.464	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,908 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.00062% 10/1,612,950 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,454
Remaining individualsnot grpmax-eligible	0.0016%	62,410
Finnishnot grpmax-eligible	0.00157%	63,750
European (non-Finnish)	0.000509%	196,580

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: B4GALT7
Protein: p.Pro80=
Coding: c.240C>T
MANE Select: NM_007255
dbSNP: rs377379133
Type: single nucleotide variant
Location: chr5:177604368 (GRCh38)
Gene constraint: LOEUF 1.228 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.70 · 2 PDB
Residue 80: the 'disordered' region

Full B4GALT7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Ehlers-Danlos syndrome, spondylodysplastic type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Spondylodysplastic Ehlers-Danlos syndrome (Orphanet):

Onset: Infancy, Neonatal
Prevalence: <1 / 1 000 000 (Worldwide)

Similar variants

B4GALT7 p.Pro80Leu Uncertain significance ★★ ⚠ same residue
B4GALT7 p.Ala186Asp Likely pathogenic ★★ same condition
B4GALT7 p.Arg270Cys Pathogenic ★★ ⚠ same condition
B4GALT7 c.413+6G>A Uncertain significance ★★ same condition
B4GALT7 p.Arg125Gln Uncertain significance ★★ ⚠ same condition
B4GALT7 p.Arg17Gly Uncertain significance ★★ ⚠ same condition
B4GALT7 p.Arg212Trp Uncertain significance ★★ ⚠ same condition
B4GALT7 p.Arg220Cys 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/b4galt7-p-pro80 (accessed [today's date]).

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