Is NEMF p.Tyr482= (c.1446T>C) pathogenic?

NEMF p.Tyr482= (c.1446T>C) is classified Likely benign in NEMF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-12-05). Rare (popmax 0.397%, sas); Associated with NEMF-related disorder.

What condition is associated with NEMF p.Tyr482= (c.1446T>C)?

NEMF p.Tyr482= (c.1446T>C) is associated with NEMF-related disorder (ClinVar).

How common is NEMF p.Tyr482= (c.1446T>C) in the general population?

NEMF p.Tyr482= (c.1446T>C) is rare (popmax 0.397%, sas) (gnomAD).

NEMF p.Tyr482=

c.1446T>C · rs369479514 · VCV3049079

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.397%, sas)

Conditions

NEMF-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 -0.91	GERP 0.36
Overall
CADD	5.013	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.397% South Asian · 355/89,364 alleles

Filtering AF 0.363% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.35%

Overall 0.026% 415/1,599,096 alleles · rare exomes 388/1,446,776 · genomes 27/152,320 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.397%	252
Middle Eastern	0.0838%	1,194
Remaining individualsnot grpmax-eligible	0.0436%	2,295
East Asian	0.0134%	7,439
Admixed American	0.00342%	29,256
African / African-American	0.00268%	37,265
European (non-Finnish)	0.00154%	64,988

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: NEMF
Protein: p.Tyr482=
Coding: c.1446T>C
MANE Select: NM_004713
dbSNP: rs369479514
Type: single nucleotide variant
Location: chr14:49828333 (GRCh38)
Gene constraint: LOEUF 0.687 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.96 · 2 PDB
Residue 482: an α-helix

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

Disease context

NEMF-related disorder

Similar variants

NEMF c.1232+4A>G Likely benign same condition
NEMF c.232-9T>C Benign same condition
NEMF c.358-7A>G Benign same condition
NEMF p.Gln386= Likely benign same condition
NEMF p.Pro944= Likely benign same condition
NEMF p.Ser817= Likely benign same condition
NEMF p.Gln445_Lys446insTer Likely pathogenic ★ same condition
NEMF p.Arg671Ter 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/nemf-p-tyr482 (accessed [today's date]).

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