Is SEMA3E p.Ser381= (c.1143T>G) pathogenic?

SEMA3E p.Ser381= (c.1143T>G) is classified Likely benign in SEMA3E (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-01-05). Absent from gnomAD v4.1; Associated with SEMA3E-related disorder.

What condition is associated with SEMA3E p.Ser381= (c.1143T>G)?

SEMA3E p.Ser381= (c.1143T>G) is associated with SEMA3E-related disorder (ClinVar).

How common is SEMA3E p.Ser381= (c.1143T>G) in the general population?

SEMA3E p.Ser381= (c.1143T>G) is absent from gnomAD v4.1 (gnomAD).

SEMA3E p.Ser381=

c.1143T>G · rs2484310463 · VCV3055428

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

SEMA3E-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 3.6	GERP -3, phastCons 1
Overall
CADD	11.17	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: SEMA3E
Protein: p.Ser381=
Coding: c.1143T>G
MANE Select: NM_012431
dbSNP: rs2484310463
Type: single nucleotide variant
Location: chr7:83402632 (GRCh38)
Gene constraint: LOEUF 0.668 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.62
Residue 381: the sema domain

Full SEMA3E gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SEMA3E-related disorder

Similar variants

SEMA3E p.Ser381Pro Uncertain significance ★ ⚠ same residue
SEMA3E p.Ala437Thr Uncertain significance ★★ ⚠ same condition
SEMA3E p.Ala609Val Uncertain significance ★★ ⚠ same condition
SEMA3E p.Arg75Gly Uncertain significance ★★ same condition
SEMA3E p.His359Arg Uncertain significance ★★ same condition
SEMA3E p.Pro161His Uncertain significance ★★ ⚠ same condition
SEMA3E p.Ser97Cys Uncertain significance ★★ ⚠ same condition
SEMA3E p.Val477Ile 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/sema3e-p-ser381 (accessed [today's date]).

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