Is ANLN p.Pro3= (c.9G>C) pathogenic?

ANLN p.Pro3= (c.9G>C) is classified Likely benign in ANLN (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-04-29). AlphaMissense: likely benign (0.1385); Ultra-rare (popmax 0.0165%, nfe); Associated with ANLN-related disorder.

What condition is associated with ANLN p.Pro3= (c.9G>C)?

ANLN p.Pro3= (c.9G>C) is associated with ANLN-related disorder (ClinVar).

How common is ANLN p.Pro3= (c.9G>C) in the general population?

ANLN p.Pro3= (c.9G>C) is ultra-rare (popmax 0.0165%, nfe) (gnomAD).

What do computational predictors say about ANLN p.Pro3= (c.9G>C)?

AlphaMissense predicts likely benign (score 0.1385) — an in-silico prediction, not a clinical call.

ANLN p.Pro3=

c.9G>C · rs372625290 · VCV3054444

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1385 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ANLN-related disorder

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.1385	likely benign
REVEL	0.039	moderately benign-leaning
SaProt	LLR -7.53	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.5	GERP 0.1, phastCons 1
Overall
CADD	19.63	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

Grpmax group 0.0165% European (non-Finnish) · 195/1,179,976 alleles

Filtering AF 0.0146% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0139%

Overall 0.0124% 200/1,613,886 alleles · ultra-rare exomes 190/1,461,670 · genomes 10/152,216 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0165%	6,051
African / African-American	0.004%	24,977
Remaining individualsnot grpmax-eligible	0.0032%	31,235

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: ANLN
Protein: p.Pro3=
Coding: c.9G>C
MANE Select: NM_018685
dbSNP: rs372625290
Type: single nucleotide variant
Location: chr7:36390035 (GRCh38)

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

Disease context

ANLN-related disorder

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/anln-p-pro3 (accessed [today's date]).

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