Is CA10 p.Asn201Asp (c.601A>G) pathogenic?

CA10 p.Asn201Asp (c.601A>G) is classified Uncertain significance in CA10 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-04). AlphaMissense: likely pathogenic (0.5901); Very rare (popmax 0.000254%, nfe).

How common is CA10 p.Asn201Asp (c.601A>G) in the general population?

CA10 p.Asn201Asp (c.601A>G) is very rare (popmax 0.000254%, nfe) (gnomAD).

What do computational predictors say about CA10 p.Asn201Asp (c.601A>G)?

AlphaMissense predicts likely pathogenic (score 0.5901) — an in-silico prediction, not a clinical call.

CA10 p.Asn201Asp

c.601A>G · rs2544054328 · VCV2316381

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5901 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.5901	likely pathogenic
REVEL	0.303	indeterminate
SaProt	LLR -7.36	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 526 kb · p 0.0032 · regional, not allelic
Overall
CADD	26.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,179,462 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000205% 3/1,461,238 alleles · very rare

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: CA10
Protein: p.Asn201Asp
Coding: c.601A>G
MANE Select: NM_020178
dbSNP: rs2544054328
Type: single nucleotide variant
Location: chr17:51649215 (GRCh38)
Gene constraint: LOEUF 0.682 · pLI 0.29 (gnomAD)
Structure: AlphaFold pLDDT 85.65
Residue 201: the alpha-carbonic anhydrase domain

Full CA10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CA10 p.Trp250Leu Uncertain significance ★★ ⚠ same type
CA10 p.Ala21Val Uncertain significance ★ ⚠ same type
CA10 p.Arg127Gln Uncertain significance ★ ⚠ same type
CA10 p.Arg198Gln Uncertain significance ★ ⚠ same type
CA10 p.Arg298Cys Uncertain significance ★ ⚠ same type
CA10 p.Arg65Gln Uncertain significance ★ ⚠ same type
CA10 p.Asn116Ser Uncertain significance ★ ⚠ same type
CA10 p.Asn14Ser 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/ca10-p-asn201asp (accessed [today's date]).

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