Is NEMF p.Pro944= (c.2832G>A) pathogenic?

NEMF p.Pro944= (c.2832G>A) is classified Likely benign in NEMF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-20). Ultra-rare (popmax 0.0401%, eas); Associated with NEMF-related disorder.

What condition is associated with NEMF p.Pro944= (c.2832G>A)?

NEMF p.Pro944= (c.2832G>A) is associated with NEMF-related disorder (ClinVar).

How common is NEMF p.Pro944= (c.2832G>A) in the general population?

NEMF p.Pro944= (c.2832G>A) is ultra-rare (popmax 0.0401%, eas) (gnomAD).

NEMF p.Pro944=

c.2832G>A · rs562458907 · VCV3058114

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0401%, eas)

Conditions

NEMF-related disorder

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 -3.2	GERP -3.4
Overall
CADD	0.609	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0401% East Asian · 18/44,890 alleles

Filtering AF 0.0258% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0213%

Overall 0.00248% 40/1,613,982 alleles · ultra-rare exomes 37/1,461,842 · genomes 3/152,140 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0401%	2,494
Remaining individualsnot grpmax-eligible	0.0064%	15,620
South Asian	0.00549%	18,216
European (non-Finnish)	0.0011%	90,770

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.Pro944=
Coding: c.2832G>A
MANE Select: NM_004713
dbSNP: rs562458907
Type: single nucleotide variant
Location: chr14:49789209 (GRCh38)
Gene constraint: LOEUF 0.687 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.96 · 2 PDB
Residue 944: a UniProt-annotated variant site (in iddsapn); the 'disordered' region

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

Disease context

NEMF-related disorder

Similar variants

NEMF p.Pro944Ala Uncertain significance ★ ⚠ same residue
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.Ser817= Likely benign same condition
NEMF p.Tyr482= Likely benign same condition
NEMF p.Gln445_Lys446insTer Likely pathogenic ★ 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/nemf-p-pro944 (accessed [today's date]).

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