Is EBLN1 p.Ser33Phe (c.98C>T) pathogenic?

EBLN1 p.Ser33Phe (c.98C>T) is classified Uncertain significance in EBLN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-01). AlphaMissense: likely benign (0.268); Absent from gnomAD v4.1.

How common is EBLN1 p.Ser33Phe (c.98C>T) in the general population?

EBLN1 p.Ser33Phe (c.98C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EBLN1 p.Ser33Phe (c.98C>T)?

AlphaMissense predicts likely benign (score 0.268) — an in-silico prediction, not a clinical call.

EBLN1 p.Ser33Phe

c.98C>T · rs1834734419 · VCV2331508

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.268 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.268	likely benign
SaProt	LLR -7.69	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.01	GERP 0.18, phastCons 0.001
Regional constraint	o/e 0.88	unconstrained · MANE · 1,097 bp · p 0.014 · regional, not allelic
Overall
CADD	18.21	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; SaProt is an independent agreement signal.

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: EBLN1
Protein: p.Ser33Phe
Coding: c.98C>T
MANE Select: NM_001394757
dbSNP: rs1834734419
Type: single nucleotide variant
Location: chr10:22209886 (GRCh38)
Gene constraint: LOEUF 1.908 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.45

Full EBLN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EBLN1 p.Ala148Val Uncertain significance ★ ⚠ same type
EBLN1 p.Ala218Val Uncertain significance ★ ⚠ same type
EBLN1 p.Ala256Thr Uncertain significance ★ ⚠ same type
EBLN1 p.Ala302Glu Uncertain significance ★ same type
EBLN1 p.Ala305Gly Uncertain significance ★ ⚠ same type
EBLN1 p.Ala309Asp Uncertain significance ★ same type
EBLN1 p.Arg138Pro Uncertain significance ★ same type
EBLN1 p.Arg199Ser Uncertain significance ★ same type

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/ebln1-p-ser33phe (accessed [today's date]).

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