Is EPHB4 p.Ser46= (c.138C>T) pathogenic?

EPHB4 p.Ser46= (c.138C>T) is classified Likely benign in EPHB4 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-05-29). Ultra-rare (popmax 0.0137%, eas); Associated with Cardiovascular phenotype.

What condition is associated with EPHB4 p.Ser46= (c.138C>T)?

EPHB4 p.Ser46= (c.138C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is EPHB4 p.Ser46= (c.138C>T) in the general population?

EPHB4 p.Ser46= (c.138C>T) is ultra-rare (popmax 0.0137%, eas) (gnomAD).

EPHB4 p.Ser46=

c.138C>T · rs564432724 · VCV2562046

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0137%, eas)

Conditions

Cardiovascular phenotype

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 -2.8	GERP -4.4
Overall
CADD	7.239	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0137% East Asian · 6/43,644 alleles

Filtering AF 0.00592% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00403%

Overall 0.00088% 14/1,590,170 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0137%	7,274
African / African-American	0.00402%	24,873
South Asian	0.00112%	88,914
European (non-Finnish)	0.000342%	292,007

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: EPHB4
Protein: p.Ser46=
Coding: c.138C>T
MANE Select: NM_004444
dbSNP: rs564432724
Type: single nucleotide variant
Location: chr7:100823917 (GRCh38)
Gene constraint: LOEUF 0.645 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.46 · 23 PDB
Residue 46: the eph lbd domain; a β-strand

Full EPHB4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EPHB4 c.1870+5G>C Uncertain significance ★★ same condition
EPHB4 p.Ala262Val Uncertain significance ★★ ⚠ same condition
EPHB4 p.Ala345Gly Uncertain significance ★★ ⚠ same condition
EPHB4 p.Ala931Thr Uncertain significance ★★ ⚠ same condition
EPHB4 p.Arg148Trp Uncertain significance ★★ ⚠ same condition
EPHB4 p.Arg310Gln Uncertain significance ★★ ⚠ same condition
EPHB4 p.Arg483Gln Uncertain significance ★★ ⚠ same condition
EPHB4 p.Arg499Gln 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/ephb4-p-ser46 (accessed [today's date]).

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