Is EFNB1 p.Pro335= (c.1005G>T) pathogenic?

EFNB1 p.Pro335= (c.1005G>T) is classified Likely benign in EFNB1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-21). Absent from gnomAD v4.1; Associated with EFNB1-related disorder.

What condition is associated with EFNB1 p.Pro335= (c.1005G>T)?

EFNB1 p.Pro335= (c.1005G>T) is associated with EFNB1-related disorder (ClinVar).

How common is EFNB1 p.Pro335= (c.1005G>T) in the general population?

EFNB1 p.Pro335= (c.1005G>T) is absent from gnomAD v4.1 (gnomAD).

EFNB1 p.Pro335=

c.1005G>T · rs770643654 · VCV3047493

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

EFNB1-related disorder

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 -0.17	GERP -4, phastCons 0.007
Overall
CADD	5.477	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EFNB1
Protein: p.Pro335=
Coding: c.1005G>T
MANE Select: NM_004429
dbSNP: rs770643654
Type: single nucleotide variant
Location: chrX:68840618 (GRCh38)
Structure: AlphaFold pLDDT 71.68 · 1 PDB

Full EFNB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EFNB1-related disorder

Similar variants

EFNB1 p.Gly151Ser Pathogenic ★★ same condition
EFNB1 p.Trp12Ter Pathogenic/Likely pathogenic ★★ same condition
EFNB1 p.Leu98Ser Likely pathogenic ★ same condition
EFNB1 p.Lys59Asn Likely pathogenic ★ same condition
EFNB1 p.Lys59Glu Likely pathogenic ★ same condition
EFNB1 p.Val164Ile Uncertain significance ★ same condition
EFNB1 p.Arg109His Uncertain significance ⚠ same condition
EFNB1 c.-6G>A Likely benign 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/efnb1-p-pro335 (accessed [today's date]).

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