Is MRPL3 p.Phe95Ser (c.284T>C) pathogenic?

MRPL3 p.Phe95Ser (c.284T>C) is classified Likely benign in MRPL3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-19). AlphaMissense: likely benign (0.0472); No allele count reported in gnomAD v4.1 (AN 1,613,406).

How common is MRPL3 p.Phe95Ser (c.284T>C) in the general population?

MRPL3 p.Phe95Ser (c.284T>C) is no allele count reported in gnomAD v4.1 (AN 1,613,406) (gnomAD).

What do computational predictors say about MRPL3 p.Phe95Ser (c.284T>C)?

AlphaMissense predicts likely benign (score 0.0472) — an in-silico prediction, not a clinical call.

MRPL3 p.Phe95Ser

c.284T>C · rs2472545877 · VCV2619363

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0472 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,406)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0472	likely benign
REVEL	0.146	moderately benign-leaning
SaProt	LLR -2.41	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.64	GERP -0.71
Regional constraint	o/e 0.95	unconstrained · MANE · 40 kb · p 0.3 · regional, not allelic
Overall
CADD	14.04	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,406). 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: MRPL3
Protein: p.Phe95Ser
Coding: c.284T>C
MANE Select: NM_007208
dbSNP: rs2472545877
Type: single nucleotide variant
Location: chr3:131500515 (GRCh38)
Gene constraint: LOEUF 1.403 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.20 · 92 PDB

Full MRPL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MRPL3 p.Ala185Val Uncertain significance ★★ ⚠ same type
MRPL3 p.Arg199His Uncertain significance ★★ ⚠ same type
MRPL3 p.Arg275Lys Uncertain significance ★★ ⚠ same type
MRPL3 p.Gly169Val Uncertain significance ★★ ⚠ same type
MRPL3 p.His117Arg Uncertain significance ★★ ⚠ same type
MRPL3 p.Ile100Thr Uncertain significance ★★ same type
MRPL3 p.Ile345Val Uncertain significance ★★ ⚠ same type
MRPL3 p.Pro171Leu 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/mrpl3-p-phe95ser (accessed [today's date]).

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