Is EPHB4 p.Thr654Met (c.1961C>T) pathogenic?

EPHB4 p.Thr654Met (c.1961C>T) is classified Conflicting classifications of pathogenicity in EPHB4 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2023-08-01). AlphaMissense: likely benign (0.2927); Very rare (popmax 0.00667%, amr); Associated with Cardiovascular phenotype.

What condition is associated with EPHB4 p.Thr654Met (c.1961C>T)?

EPHB4 p.Thr654Met (c.1961C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is EPHB4 p.Thr654Met (c.1961C>T) in the general population?

EPHB4 p.Thr654Met (c.1961C>T) is very rare (popmax 0.00667%, amr) (gnomAD).

What do computational predictors say about EPHB4 p.Thr654Met (c.1961C>T)?

AlphaMissense predicts likely benign (score 0.2927) — an in-silico prediction, not a clinical call.

EPHB4 p.Thr654Met

c.1961C>T · rs765067395 · VCV2462871

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2927 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00667%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.2927	likely benign
REVEL	0.693	pathogenic-leaning
SaProt	LLR -9.78	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 0.61	unconstrained · MANE · 6,734 bp · p 5.4e-12 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00667% Admixed American · 4/60,000 alleles

Filtering AF 0.00275% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00244%

Overall 0.00322% 52/1,614,096 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00667%	15,000
Remaining individualsnot grpmax-eligible	0.0048%	20,829
European (non-Finnish)	0.00364%	27,443
South Asian	0.0022%	45,545

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.Thr654Met
Coding: c.1961C>T
MANE Select: NM_004444
dbSNP: rs765067395
Type: single nucleotide variant
Location: chr7:100812904 (GRCh38)
Gene constraint: LOEUF 0.645 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.46 · 23 PDB
Residue 654: a UniProt-annotated variant site (in cmavm2); the protein kinase domain

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 p.Thr654= Likely benign ★ same residue
EPHB4 p.Thr654Ser Uncertain significance ★ ⚠ same residue
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

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-thr654met (accessed [today's date]).

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