Is CATSPERB p.Phe511Ser (c.1532T>C) pathogenic?

CATSPERB p.Phe511Ser (c.1532T>C) is classified Uncertain significance in CATSPERB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-27). AlphaMissense: likely benign (0.1913); Absent from gnomAD v4.1.

How common is CATSPERB p.Phe511Ser (c.1532T>C) in the general population?

CATSPERB p.Phe511Ser (c.1532T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CATSPERB p.Phe511Ser (c.1532T>C)?

AlphaMissense predicts likely benign (score 0.1913) — an in-silico prediction, not a clinical call.

CATSPERB p.Phe511Ser

c.1532T>C · rs2542388917 · VCV3137792

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1913 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1913	likely benign
REVEL	0.166	moderately benign-leaning
SaProt	LLR -5.20	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 2.9	GERP -0.8, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 149 kb · p 1.3e-06 · regional, not allelic
Overall
CADD	17.27	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: CATSPERB
Protein: p.Phe511Ser
Coding: c.1532T>C
MANE Select: NM_024764
dbSNP: rs2542388917
Type: single nucleotide variant
Location: chr14:91639151 (GRCh38)
Gene constraint: LOEUF 0.935 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.99

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

Similar variants

CATSPERB p.Ala127Val Uncertain significance ★ ⚠ same type
CATSPERB p.Ala190Asp Uncertain significance ★ ⚠ same type
CATSPERB p.Ala304Val Uncertain significance ★ ⚠ same type
CATSPERB p.Ala444Asp Uncertain significance ★ ⚠ same type
CATSPERB p.Ala444Thr Uncertain significance ★ ⚠ same type
CATSPERB p.Ala462Gly Uncertain significance ★ ⚠ same type
CATSPERB p.Ala519Thr Uncertain significance ★ ⚠ same type
CATSPERB p.Ala681Thr 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/catsperb-p-phe511ser (accessed [today's date]).

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