Is SEMA3A p.Pro768= (c.2304C>T) pathogenic?

SEMA3A p.Pro768= (c.2304C>T) is classified Likely benign in SEMA3A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-04-08). Absent from gnomAD v4.1; Associated with SEMA3A-related disorder.

What condition is associated with SEMA3A p.Pro768= (c.2304C>T)?

SEMA3A p.Pro768= (c.2304C>T) is associated with SEMA3A-related disorder (ClinVar).

How common is SEMA3A p.Pro768= (c.2304C>T) in the general population?

SEMA3A p.Pro768= (c.2304C>T) is absent from gnomAD v4.1 (gnomAD).

SEMA3A p.Pro768=

c.2304C>T · VCV3357760

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

SEMA3A-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 1.8	GERP 2, phastCons 1
Overall
CADD	7.698	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: SEMA3A
Protein: p.Pro768=
Coding: c.2304C>T
MANE Select: NM_006080
Type: single nucleotide variant
Location: chr7:83961383 (GRCh38)
Gene constraint: LOEUF 0.453 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 84.50
Residue 768: the 'disordered' region

Full SEMA3A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SEMA3A-related disorder

Similar variants

SEMA3A p.Ala523Val Uncertain significance ★★ ⚠ same condition
SEMA3A p.Arg617Ter Uncertain significance ★★ same condition
SEMA3A p.Ile421Met Uncertain significance ★★ ⚠ same condition
SEMA3A p.Pro374His Uncertain significance ★★ ⚠ same condition
SEMA3A c.1860+1G>A Pathogenic ★ same condition
SEMA3A p.Glu589Gln Uncertain significance ★ ⚠ same condition
SEMA3A p.Trp3Cys Uncertain significance ★ ⚠ same condition
SEMA3A p.Val243Ile 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/sema3a-p-pro768 (accessed [today's date]).

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