Is COBL p.Pro148Ser (c.442C>T) pathogenic?

COBL p.Pro148Ser (c.442C>T) is classified Uncertain significance in COBL (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-09). AlphaMissense: likely benign (0.0773); Ultra-rare (popmax 0.0334%, afr).

How common is COBL p.Pro148Ser (c.442C>T) in the general population?

COBL p.Pro148Ser (c.442C>T) is ultra-rare (popmax 0.0334%, afr) (gnomAD).

What do computational predictors say about COBL p.Pro148Ser (c.442C>T)?

AlphaMissense predicts likely benign (score 0.0773) — an in-silico prediction, not a clinical call.

COBL p.Pro148Ser

c.442C>T · VCV4004770

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0773 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0334%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0773	likely benign
REVEL	0.218	benign-leaning
SaProt	LLR -9.59	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.5	GERP 0.24, phastCons 0.81
Regional constraint	o/e 1.11	unconstrained · MANE · 126 kb · p 0.12 · regional, not allelic
Overall
CADD	15.06	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

Grpmax group 0.0334% African / African-American · 25/74,906 alleles

Filtering AF 0.0231% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0198%

Overall 0.00167% 27/1,614,026 alleles · ultra-rare exomes 10/1,461,862 · genomes 17/152,164 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0334%	2,996
Admixed American	0.00167%	59,998
Remaining individualsnot grpmax-eligible	0.0016%	62,488

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: COBL
Protein: p.Pro148Ser
Coding: c.442C>T
MANE Select: NM_015198
Type: single nucleotide variant
Location: chr7:51193393 (GRCh38)
Gene constraint: LOEUF 0.638 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 50.88 · 1 PDB

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

Similar variants

COBL p.Pro148Leu Uncertain significance ★ ⚠ same residue
COBL p.Ala57= Benign ★★ same type
COBL p.Ala655Pro Benign ★★ same type
COBL p.Gly534Ser Likely benign ★★ same type
COBL p.His601Tyr Benign ★★ same type
COBL p.Ser47= Benign ★★ same type
COBL p.Ser513Phe Benign ★★ same type
COBL p.Thr1234= Benign ★★ 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/cobl-p-pro148ser (accessed [today's date]).

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