Is CAMTA1 p.Ser899= (c.2697C>T) pathogenic?

CAMTA1 p.Ser899= (c.2697C>T) is classified Likely benign in CAMTA1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-16). Very rare (popmax 0.00801%, afr); Associated with CAMTA1-related disorder.

What condition is associated with CAMTA1 p.Ser899= (c.2697C>T)?

CAMTA1 p.Ser899= (c.2697C>T) is associated with CAMTA1-related disorder (ClinVar).

How common is CAMTA1 p.Ser899= (c.2697C>T) in the general population?

CAMTA1 p.Ser899= (c.2697C>T) is very rare (popmax 0.00801%, afr) (gnomAD).

CAMTA1 p.Ser899=

c.2697C>T · rs372047367 · VCV3049723

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

Conditions

CAMTA1-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 4	GERP 1.5, phastCons 1
Overall
CADD	12.68	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,914 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.000558% 9/1,613,688 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00801%	12,486
European (non-Finnish)	0.000254%	393,323

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: CAMTA1
Protein: p.Ser899=
Coding: c.2697C>T
MANE Select: NM_015215
dbSNP: rs372047367
Type: single nucleotide variant
Location: chr1:7670955 (GRCh38)
Gene constraint: LOEUF 0.227 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 51.94 · 1 PDB
Residue 899: the ipt/tig domain

Full CAMTA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CAMTA1-related disorder

Similar variants

CAMTA1 c.3342+1G>T Likely pathogenic ★★ same condition
CAMTA1 p.Ala588Thr Uncertain significance ★★ ⚠ same condition
CAMTA1 p.Arg284His Uncertain significance ★★ ⚠ same condition
CAMTA1 p.Arg811Trp Uncertain significance ★★ ⚠ same condition
CAMTA1 c.3067-1G>A Likely pathogenic ★ same condition
CAMTA1 p.Gly391Arg Uncertain significance ★ ⚠ same condition
CAMTA1 p.Leu1143Ile Uncertain significance ★ ⚠ same condition
CAMTA1 p.Met758Leu Uncertain significance ★ ⚠ 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/camta1-p-ser899 (accessed [today's date]).

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