Is BABAM1 p.Pro9Arg (c.26C>G) pathogenic?

BABAM1 p.Pro9Arg (c.26C>G) is classified Uncertain significance in BABAM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-13). AlphaMissense: likely benign (0.1094); Absent from gnomAD v4.1.

How common is BABAM1 p.Pro9Arg (c.26C>G) in the general population?

BABAM1 p.Pro9Arg (c.26C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BABAM1 p.Pro9Arg (c.26C>G)?

AlphaMissense predicts likely benign (score 0.1094) — an in-silico prediction, not a clinical call.

BABAM1 p.Pro9Arg

c.26C>G · VCV3984060

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1094 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1094	likely benign
REVEL	0.034	moderately benign-leaning
SaProt	LLR -5.60	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 4.5	GERP -1.6, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 10 kb · p 0.049 · regional, not allelic
Overall
CADD	21.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BABAM1
Protein: p.Pro9Arg
Coding: c.26C>G
MANE Select: NM_014173
Type: single nucleotide variant
Location: chr19:17268832 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 79.21 · 10 PDB
Residue 9: the 'disordered' region

Full BABAM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BABAM1 c.-13-45C>T Benign ★★ same type
BABAM1 p.Ala283Thr Uncertain significance ★ ⚠ same type
BABAM1 p.Arg212His Uncertain significance ★ ⚠ same type
BABAM1 p.Arg212Pro Uncertain significance ★ ⚠ same type
BABAM1 p.Arg219Cys Uncertain significance ★ ⚠ same type
BABAM1 p.Arg26Cys Uncertain significance ★ ⚠ same type
BABAM1 p.Arg85Gln Uncertain significance ★ ⚠ same type
BABAM1 p.Asn122Ser 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/babam1-p-pro9arg (accessed [today's date]).

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