Is EFNB1 p.Trp8Ter (c.24G>A) pathogenic?

EFNB1 p.Trp8Ter (c.24G>A) is classified Likely pathogenic in EFNB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-05-20). Absent from gnomAD v4.1; Associated with craniofrontonasal syndrome.

What condition is associated with EFNB1 p.Trp8Ter (c.24G>A)?

EFNB1 p.Trp8Ter (c.24G>A) is associated with craniofrontonasal syndrome (ClinVar).

How common is EFNB1 p.Trp8Ter (c.24G>A) in the general population?

EFNB1 p.Trp8Ter (c.24G>A) is absent from gnomAD v4.1 (gnomAD).

EFNB1 p.Trp8Ter

c.24G>A · rs2080439314 · VCV929457

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,191,734)

Conditions

craniofrontonasal syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 1 of 5
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.5, phastCons 1
Overall
CADD	38.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,191,734). 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: EFNB1
Protein: p.Trp8Ter
Coding: c.24G>A
MANE Select: NM_004429
dbSNP: rs2080439314
Type: single nucleotide variant
Location: chrX:68829800 (GRCh38)
Structure: AlphaFold pLDDT 71.68 · 1 PDB

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

Disease context

craniofrontonasal syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EFNB1 c.128+1G>C Likely pathogenic ★★ same condition
EFNB1 c.499+1G>A Pathogenic/Likely pathogenic ★★ same condition
EFNB1 p.Arg66Ter Pathogenic ★★ same condition
EFNB1 p.Gln175Ter Likely pathogenic ★★ same condition
EFNB1 p.Gln85Ter Pathogenic ★★ same condition
EFNB1 p.Gly151Ser Pathogenic ★★ same condition
EFNB1 p.Met158Val Pathogenic/Likely pathogenic ★★ same condition
EFNB1 p.Met1Val 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/efnb1-p-trp8ter (accessed [today's date]).

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