Is SEMA3B p.Pro685= (c.2055C>T) pathogenic?

SEMA3B p.Pro685= (c.2055C>T) is classified Uncertain significance in SEMA3B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-05-24). No allele count reported in gnomAD v4.1 (AN 1,533,162); Associated with SEMA3B-related disorder.

What condition is associated with SEMA3B p.Pro685= (c.2055C>T)?

SEMA3B p.Pro685= (c.2055C>T) is associated with SEMA3B-related disorder (ClinVar).

How common is SEMA3B p.Pro685= (c.2055C>T) in the general population?

SEMA3B p.Pro685= (c.2055C>T) is no allele count reported in gnomAD v4.1 (AN 1,533,162) (gnomAD).

SEMA3B p.Pro685=

c.2055C>T · VCV3346848

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,533,162)

Conditions

SEMA3B-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 0.39	GERP -2.6, phastCons 0.99
Overall
CADD	11.08	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,533,162). 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: SEMA3B
Protein: p.Pro685=
Coding: c.2055C>T
MANE Select: NM_001290060
Type: single nucleotide variant
Location: chr3:50276511 (GRCh38)
Gene constraint: LOEUF 1.219 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.84

Full SEMA3B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SEMA3B-related disorder

Similar variants

SEMA3B p.Ala680Val Likely benign ★★ same condition
SEMA3B p.Arg148Trp Uncertain significance ★ ⚠ same condition
SEMA3B p.Arg371Cys Uncertain significance ★ ⚠ same condition
SEMA3B p.Arg418Ser Uncertain significance ★ ⚠ same condition
SEMA3B p.Arg728Gly Uncertain significance ★ ⚠ same condition
SEMA3B p.Asn221Lys Uncertain significance ★ ⚠ same condition
SEMA3B p.Gly568= Uncertain significance ★ same condition
SEMA3B p.Gly650Asp 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/sema3b-p-pro685 (accessed [today's date]).

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