Is MRPS2 p.Lys68= (c.204G>A) pathogenic?

MRPS2 p.Lys68= (c.204G>A) is classified Likely benign in MRPS2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-03). Very rare (popmax 0.00833%, amr); Associated with MRPS2-related disorder.

What condition is associated with MRPS2 p.Lys68= (c.204G>A)?

MRPS2 p.Lys68= (c.204G>A) is associated with MRPS2-related disorder (ClinVar).

How common is MRPS2 p.Lys68= (c.204G>A) in the general population?

MRPS2 p.Lys68= (c.204G>A) is very rare (popmax 0.00833%, amr) (gnomAD).

MRPS2 p.Lys68=

c.204G>A · rs772577776 · VCV3047417

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00833%, amr)

Conditions

MRPS2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.29	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 2.5	GERP 2.5, phastCons 1
Overall
CADD	15.95	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00833% Admixed American · 5/60,008 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.000682% 11/1,613,682 alleles · very rare exomes 8/1,461,466 · genomes 3/152,216 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00833%	12,002
Remaining individualsnot grpmax-eligible	0.0016%	62,472
African / African-American	0.00133%	74,944
European (non-Finnish)	0.000339%	294,994

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MRPS2
Protein: p.Lys68=
Coding: c.204G>A
MANE Select: NM_016034
dbSNP: rs772577776
Type: single nucleotide variant
Location: chr9:135501878 (GRCh38)
Gene constraint: LOEUF 1.166 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.27 · 86 PDB
Residue 68: an α-helix

Full MRPS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MRPS2-related disorder

Similar variants

MRPS2 p.Lys68Arg Uncertain significance ★ ⚠ same residue
MRPS2 c.170-4G>A Likely benign same condition
MRPS2 p.Arg88Gln Uncertain significance ★★ ⚠ same type
MRPS2 p.Gly24Asp Uncertain significance ★★ ⚠ same type
MRPS2 p.His134Tyr Uncertain significance ★★ same type
MRPS2 p.Pro243Leu Uncertain significance ★★ ⚠ same type
MRPS2 p.Ser5Leu Uncertain significance ★★ ⚠ same type
MRPS2 p.Trp22Ter 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/mrps2-p-lys68 (accessed [today's date]).

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