Is DYSF p.Ser241Phe (c.722C>T) pathogenic?

DYSF p.Ser241Phe (c.722C>T) is classified Uncertain significance in DYSF (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-06-01). AlphaMissense: likely benign (0.1548); Very rare (popmax 0.00161%, nfe).

How common is DYSF p.Ser241Phe (c.722C>T) in the general population?

DYSF p.Ser241Phe (c.722C>T) is very rare (popmax 0.00161%, nfe) (gnomAD).

What do computational predictors say about DYSF p.Ser241Phe (c.722C>T)?

AlphaMissense predicts likely benign (score 0.1548) — an in-silico prediction, not a clinical call.

DYSF p.Ser241Phe

c.722C>T · rs754343148 · VCV283252

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1548 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00161%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1548	likely benign
REVEL	0.17	moderately benign-leaning
SaProt	LLR -7.52	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 5.4	GERP 1.9, phastCons 0.99
Regional constraint	o/e 1.02	unconstrained · MANE · 85 kb · p 0.54 · regional, not allelic
Overall
CADD	22.3	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.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S209F vs ClinVar S241F) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00161% European (non-Finnish) · 19/1,180,046 alleles

Filtering AF 0.00103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00083%

Overall 0.00137% 20/1,461,892 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00161%	62,108
Remaining individualsnot grpmax-eligible	0.0016%	62,502

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: DYSF
Protein: p.Ser241Phe
Coding: c.722C>T
MANE Select: NM_001130987
dbSNP: rs754343148
Type: single nucleotide variant
Location: chr2:71513884 (GRCh38)
Gene constraint: LOEUF 0.836 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.25 · 11 PDB
Residue 241: a β-strand; the c2 2 domain

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

Similar variants

DYSF c.1003-3C>A Pathogenic ★★★ same type
DYSF c.1033+1G>A Pathogenic ★★★ same type
DYSF c.1033+4A>T Likely pathogenic ★★★ same type
DYSF c.1033+5G>A Likely pathogenic ★★★ same type
DYSF c.1149+1G>A Pathogenic ★★★ same type
DYSF c.1149+1G>C Pathogenic ★★★ same type
DYSF c.1149+4A>G Pathogenic ★★★ same type
DYSF c.1149+5G>A Pathogenic ★★★ 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/dysf-p-ser241phe (accessed [today's date]).

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