Is MOK p.Ser260Phe (c.779C>T) pathogenic?

MOK p.Ser260Phe (c.779C>T) is classified Uncertain significance in MOK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-24). AlphaMissense: likely benign (0.1519); Very rare (popmax 0.005%, amr).

How common is MOK p.Ser260Phe (c.779C>T) in the general population?

MOK p.Ser260Phe (c.779C>T) is very rare (popmax 0.005%, amr) (gnomAD).

What do computational predictors say about MOK p.Ser260Phe (c.779C>T)?

AlphaMissense predicts likely benign (score 0.1519) — an in-silico prediction, not a clinical call.

MOK p.Ser260Phe

c.779C>T · rs753928824 · VCV3196065

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1519 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1519	likely benign
REVEL	0.278	benign-leaning
SaProt	LLR -12.45	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.3	GERP 2.1, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 76 kb · p 0.69 · regional, not allelic
Overall
CADD	26.3	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

Grpmax group 0.005% Admixed American · 3/60,002 alleles

Filtering AF 0.00145% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00123%

Overall 0.00186% 30/1,614,044 alleles · very rare exomes 25/1,461,858 · genomes 5/152,186 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	20,001
European (non-Finnish)	0.00212%	47,201
Remaining individualsnot grpmax-eligible	0.0016%	62,478
African / African-American	0.00133%	74,918

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: MOK
Protein: p.Ser260Phe
Coding: c.779C>T
MANE Select: NM_014226
dbSNP: rs753928824
Type: single nucleotide variant
Location: chr14:102232622 (GRCh38)
Gene constraint: LOEUF 1.292 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.98
Residue 260: the protein kinase domain

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

Similar variants

MOK p.Lys137Asn Benign ★★ ⚠ same type
MOK p.Ala196Ser Uncertain significance ★ ⚠ same type
MOK p.Ala222Thr Uncertain significance ★ ⚠ same type
MOK p.Ala276Thr Uncertain significance ★ ⚠ same type
MOK p.Arg150Gln Uncertain significance ★ ⚠ same type
MOK p.Arg150Trp Uncertain significance ★ ⚠ same type
MOK p.Arg165Cys Uncertain significance ★ ⚠ same type
MOK p.Arg168Trp 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/mok-p-ser260phe (accessed [today's date]).

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