Is CBARP p.Thr6Ser (c.16A>T) pathogenic?

CBARP p.Thr6Ser (c.16A>T) is classified Uncertain significance in CBARP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-18). AlphaMissense: likely benign (0.1914); Absent from gnomAD v4.1.

How common is CBARP p.Thr6Ser (c.16A>T) in the general population?

CBARP p.Thr6Ser (c.16A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CBARP p.Thr6Ser (c.16A>T)?

AlphaMissense predicts likely benign (score 0.1914) — an in-silico prediction, not a clinical call.

CBARP p.Thr6Ser

c.16A>T · rs2512979327 · VCV3137927

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1914 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.1914	likely benign
SaProt	LLR -7.65	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.2	GERP 1, phastCons 1
Regional constraint	o/e 1.17	unconstrained · MANE · 6,918 bp · p 1.2e-07 · regional, not allelic
Overall
CADD	17.47	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: CBARP
Protein: p.Thr6Ser
Coding: c.16A>T
MANE Select: NM_001393918
dbSNP: rs2512979327
Type: single nucleotide variant
Location: chr19:1236085 (GRCh38)
Gene constraint: LOEUF 1.107 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 52.23

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

Similar variants

CBARP p.Thr6Ala Likely benign ★ same residue
CBARP p.Arg535= Likely benign ★★ same type
CBARP c.1154+114C>G Uncertain significance ★ same type
CBARP c.1154+126G>T Uncertain significance ★ same type
CBARP c.1154+36C>G Uncertain significance ★ same type
CBARP c.1154+45C>T Uncertain significance ★ same type
CBARP c.1154+80G>A Uncertain significance ★ same type
CBARP c.1154+87C>T 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/cbarp-p-thr6ser (accessed [today's date]).

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