Is CARD10 p.Arg1024Ser (c.3072A>C) pathogenic?

CARD10 p.Arg1024Ser (c.3072A>C) is classified Uncertain significance in CARD10 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-13). AlphaMissense: likely benign (0.1231); Absent from gnomAD v4.1.

How common is CARD10 p.Arg1024Ser (c.3072A>C) in the general population?

CARD10 p.Arg1024Ser (c.3072A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CARD10 p.Arg1024Ser (c.3072A>C)?

AlphaMissense predicts likely benign (score 0.1231) — an in-silico prediction, not a clinical call.

CARD10 p.Arg1024Ser

c.3072A>C · rs2517793119 · VCV2283811

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1231 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,570,016)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1231	likely benign
REVEL	0.032	moderately benign-leaning
SaProt	LLR -5.49	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 -5.6	GERP -3.1
Regional constraint	o/e 0.91	unconstrained · MANE · 25 kb · p 0.0012 · regional, not allelic
Overall
CADD	0.004	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

No allele count reported in gnomAD v4.1 (AN 1,570,016). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CARD10
Protein: p.Arg1024Ser
Coding: c.3072A>C
MANE Select: NM_014550
dbSNP: rs2517793119
Type: single nucleotide variant
Location: chr22:37491186 (GRCh38)
Gene constraint: LOEUF 0.678 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.22

Full CARD10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CARD10 p.Thr436Met Uncertain significance ★★ ⚠ same type
CARD10 p.Ala382Thr Benign ★★ same type
CARD10 p.Glu327= Likely benign ★★ same type
CARD10 p.Ile940= Benign/Likely benign ★★ same type
CARD10 p.Lys514Arg Benign ★★ same type
CARD10 p.Thr383= Benign ★★ same type
CARD10 p.Arg420Cys Likely pathogenic ★ ⚠ same type
CARD10 c.2864+2T>G 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/card10-p-arg1024ser (accessed [today's date]).

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