Is CARD10 p.Ser480= (c.1440C>T) pathogenic?

CARD10 p.Ser480= (c.1440C>T) is classified Benign in CARD10 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2019-03-06). Rare (popmax 0.101%, mid); Associated with CARD10-related disorder.

What condition is associated with CARD10 p.Ser480= (c.1440C>T)?

CARD10 p.Ser480= (c.1440C>T) is associated with CARD10-related disorder (ClinVar).

How common is CARD10 p.Ser480= (c.1440C>T) in the general population?

CARD10 p.Ser480= (c.1440C>T) is rare (popmax 0.101%, mid) (gnomAD).

CARD10 p.Ser480=

c.1440C>T · rs150575230 · VCV3050006

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.101%, mid)

Conditions

CARD10-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.91	GERP -2.8
Overall
CADD	11.71	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.101% Middle Eastern · 6/5,958 alleles

Filtering AF 0.0499% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.044%

Overall 0.0749% 1,186/1,583,712 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	2.33%	43
Remaining individualsnot grpmax-eligible	0.175%	571
Middle Easterngrpmax	0.101%	993
Admixed American	0.0669%	1,494
East Asian	0.0492%	2,032
European (non-Finnish)	0.0296%	3,381
South Asian	0.00929%	10,764
African / African-American	0.0068%	14,708

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CARD10
Protein: p.Ser480=
Coding: c.1440C>T
MANE Select: NM_014550
dbSNP: rs150575230
Type: single nucleotide variant
Location: chr22:37504713 (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

Disease context

CARD10-related disorder

Similar variants

CARD10 p.Ala1032Asp Uncertain significance ⚠ same condition
CARD10 p.Glu1019Gln Uncertain significance ⚠ same condition
CARD10 c.1383+7G>A Likely benign same condition
CARD10 c.2477-7G>C Likely benign same condition
CARD10 c.910-6C>T Benign same condition
CARD10 p.Ala528= Benign same condition
CARD10 p.Ala7= Likely benign same condition
CARD10 p.Ala704= Likely benign same condition

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-ser480 (accessed [today's date]).

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