Is NOM1 p.Ser73Arg (c.219C>G) pathogenic?

NOM1 p.Ser73Arg (c.219C>G) is classified Likely benign in NOM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-15). AlphaMissense: likely benign (0.0895); No allele count reported in gnomAD v4.1 (AN 1,541,596).

How common is NOM1 p.Ser73Arg (c.219C>G) in the general population?

NOM1 p.Ser73Arg (c.219C>G) is no allele count reported in gnomAD v4.1 (AN 1,541,596) (gnomAD).

What do computational predictors say about NOM1 p.Ser73Arg (c.219C>G)?

AlphaMissense predicts likely benign (score 0.0895) — an in-silico prediction, not a clinical call.

NOM1 p.Ser73Arg

c.219C>G · VCV3406634

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0895 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,541,596)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0895	likely benign
REVEL	0.019	moderately benign-leaning
SaProt	LLR -6.24	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 0.034	GERP -0.98, phastCons 0.001
Regional constraint	o/e 1.08	unconstrained · MANE · 20 kb · p 0.0051 · regional, not allelic
Overall
CADD	6.369	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

No allele count reported in gnomAD v4.1 (AN 1,541,596). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: NOM1
Protein: p.Ser73Arg
Coding: c.219C>G
MANE Select: NM_138400
Type: single nucleotide variant
Location: chr7:156949956 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.73
Residue 73: the 'necessary for nucleolar localization and for targeting ppp1ca to the nucleolus' region; the 'disordered' region

Full NOM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

NOM1 p.Ala102Val Uncertain significance ★ ⚠ same type
NOM1 p.Ala133Val Uncertain significance ★ ⚠ same type
NOM1 p.Ala156Val Uncertain significance ★ ⚠ same type
NOM1 p.Ala164Thr Uncertain significance ★ ⚠ same type
NOM1 p.Ala166Val Uncertain significance ★ ⚠ same type
NOM1 p.Ala168Thr Uncertain significance ★ ⚠ same type
NOM1 p.Ala170Thr Uncertain significance ★ ⚠ same type
NOM1 p.Ala273Gly 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/nom1-p-ser73arg (accessed [today's date]).

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