Is SRPRB p.Val102Ile (c.304G>A) pathogenic?

SRPRB p.Val102Ile (c.304G>A) is classified Uncertain significance in SRPRB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-15). AlphaMissense: likely benign (0.0734); Absent from gnomAD v4.1.

How common is SRPRB p.Val102Ile (c.304G>A) in the general population?

SRPRB p.Val102Ile (c.304G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SRPRB p.Val102Ile (c.304G>A)?

AlphaMissense predicts likely benign (score 0.0734) — an in-silico prediction, not a clinical call.

SRPRB p.Val102Ile

c.304G>A · VCV3322673

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0734 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0734	likely benign
REVEL	0.035	moderately benign-leaning
SaProt	LLR -8.30	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.007	GERP -1.9
Regional constraint	o/e 0.99	unconstrained · MANE · 14 kb · p 0.83 · regional, not allelic
Overall
CADD	7.772	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; REVEL and SaProt are independent agreement signals.

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: SRPRB
Protein: p.Val102Ile
Coding: c.304G>A
MANE Select: NM_001379313
Type: single nucleotide variant
Location: chr3:133807800 (GRCh38)
Gene constraint: LOEUF 1.05 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.30 · 1 PDB
Residue 102: a β-strand

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

Similar variants

SRPRB p.Ala211Val Uncertain significance ★ ⚠ same type
SRPRB p.Arg109Lys Uncertain significance ★ ⚠ same type
SRPRB p.Arg150Gln Uncertain significance ★ ⚠ same type
SRPRB p.Arg208His Uncertain significance ★ ⚠ same type
SRPRB p.Arg58Gln Uncertain significance ★ ⚠ same type
SRPRB p.Asn106Ser Uncertain significance ★ ⚠ same type
SRPRB p.Asn171Ser Uncertain significance ★ ⚠ same type
SRPRB p.Asn171Thr 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/srprb-p-val102ile (accessed [today's date]).

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