Is MOBP p.Lys96= (c.288G>A) pathogenic?

MOBP p.Lys96= (c.288G>A) is classified Likely benign in MOBP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-06-18). Very rare (popmax 0.00186%, amr); Associated with MOBP-related disorder.

What condition is associated with MOBP p.Lys96= (c.288G>A)?

MOBP p.Lys96= (c.288G>A) is associated with MOBP-related disorder (ClinVar).

How common is MOBP p.Lys96= (c.288G>A) in the general population?

MOBP p.Lys96= (c.288G>A) is very rare (popmax 0.00186%, amr) (gnomAD).

MOBP p.Lys96=

c.288G>A · VCV3348263

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00186%, amr)

Conditions

MOBP-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 0.33	GERP 0.87, phastCons 0.81
Overall
CADD	13.69	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00186% Admixed American · 1/53,862 alleles

Filtering AF 0.000508% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000371%

Overall 0.000833% 13/1,560,690 alleles · very rare exomes 11/1,408,798 · genomes 2/151,892 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00186%	53,862
Remaining individualsnot grpmax-eligible	0.00164%	61,048
European (non-Finnish)	0.000947%	105,646

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: MOBP
Protein: p.Lys96=
Coding: c.288G>A
MANE Select: NM_001393704
Type: single nucleotide variant
Location: chr3:39502616 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI 0.81 (gnomAD)
Structure: AlphaFold pLDDT 55.69
Residue 96: the 'disordered' region

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

Disease context

MOBP-related disorder

Similar variants

MOBP c.206+5G>C Uncertain significance ★ same condition
MOBP p.Pro84Ser Uncertain significance ★ ⚠ same condition
MOBP p.Pro87Leu Uncertain significance ★ ⚠ same condition
MOBP c.207-27G>A Likely benign ★ same condition
MOBP c.207-22C>T Uncertain significance same condition
MOBP p.Pro121Ser Likely benign ⚠ same condition
MOBP p.Pro152= Likely benign same condition
MOBP p.Pro80= Likely benign 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/mobp-p-lys96 (accessed [today's date]).

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