Is NSUN2 p.Ser244= (c.732C>T) pathogenic?

NSUN2 p.Ser244= (c.732C>T) is classified Likely benign in NSUN2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-09). Rare (popmax 0.16%, sas); Associated with Inborn genetic diseases.

What condition is associated with NSUN2 p.Ser244= (c.732C>T)?

NSUN2 p.Ser244= (c.732C>T) is associated with Inborn genetic diseases (ClinVar).

How common is NSUN2 p.Ser244= (c.732C>T) in the general population?

NSUN2 p.Ser244= (c.732C>T) is rare (popmax 0.16%, sas) (gnomAD).

NSUN2 p.Ser244=

c.732C>T · rs535568776 · VCV588659

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.16%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.4	GERP 1.6, phastCons 1
Overall
CADD	11.83	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.16% South Asian · 145/90,818 alleles

Filtering AF 0.138% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.13%

Overall 0.00955% 154/1,613,028 alleles · rare exomes 148/1,460,722 · genomes 6/152,306 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.16%	626
Middle Eastern	0.033%	3,029
Remaining individualsnot grpmax-eligible	0.00961%	10,406
European (non-Finnish)	8.48e-05%	1,179,569

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: NSUN2
Protein: p.Ser244=
Coding: c.732C>T
MANE Select: NM_017755
dbSNP: rs535568776
Type: single nucleotide variant
Location: chr5:6620189 (GRCh38)
Gene constraint: LOEUF 0.965 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.09 · 11 PDB

Full NSUN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NSUN2 p.Ala485Val Uncertain significance ★★ ⚠ same condition
NSUN2 p.Ala649Thr Uncertain significance ★★ ⚠ same condition
NSUN2 p.Arg175Trp Uncertain significance ★★ ⚠ same condition
NSUN2 p.Arg389Gln Uncertain significance ★★ ⚠ same condition
NSUN2 p.Arg438His Uncertain significance ★★ ⚠ same condition
NSUN2 p.Arg737Thr Uncertain significance ★★ ⚠ same condition
NSUN2 p.Arg8Gln Uncertain significance ★★ ⚠ same condition
NSUN2 p.Asn547Asp Uncertain significance ★★ ⚠ 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/nsun2-p-ser244 (accessed [today's date]).

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