Is EBP p.Gly161Arg (c.481G>A) pathogenic?

EBP p.Gly161Arg (c.481G>A) is classified Likely pathogenic in EBP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-04-05). AlphaMissense: likely pathogenic (0.9203); Absent from gnomAD v4.1; Associated with EBP-related disorders.

What condition is associated with EBP p.Gly161Arg (c.481G>A)?

EBP p.Gly161Arg (c.481G>A) is associated with EBP-related disorders, X-linked chondrodysplasia punctata 2 (ClinVar).

How common is EBP p.Gly161Arg (c.481G>A) in the general population?

EBP p.Gly161Arg (c.481G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EBP p.Gly161Arg (c.481G>A)?

AlphaMissense predicts likely pathogenic (score 0.9203) — an in-silico prediction, not a clinical call.

EBP p.Gly161Arg

c.481G>A · rs587783617 · VCV158550

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9203 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,210,874)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

EBP-related disorders

Computational evidence

Protein change
AlphaMissense	0.9203	likely pathogenic ✓ concordant with ClinVar · top 4% in EBP
REVEL	0.976	strongly pathogenic-leaning
SaProt	LLR -18.29	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	Δ0.34	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 8.4	GERP 2.1, phastCons 1
Overall
CADD	33.0	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

No allele count reported in gnomAD v4.1 (AN 1,210,874). 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: EBP
Protein: p.Gly161Arg
Coding: c.481G>A
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs587783617
Type: single nucleotide variant
Location: chrX:48528245 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 161: the 'disordered' region

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

Disease context

EBP-related disorders

Also linked: X-linked chondrodysplasia punctata 2

Similar variants

EBP p.Gly161Glu Likely pathogenic ★ same residue
EBP p.Gly161= Uncertain significance ★ same residue
EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same condition
EBP p.Arg110Ter Pathogenic ★★ same condition
EBP p.Arg147His Pathogenic ★★ ⚠ same condition
EBP p.Arg62Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
EBP p.Glu80Lys Pathogenic/Likely pathogenic ★★ same condition
EBP p.Trp186Ter Pathogenic ★★ 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/ebp-p-gly161arg (accessed [today's date]).

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