Is CA5A p.Asn45Lys (c.135T>A) pathogenic?

CA5A p.Asn45Lys (c.135T>A) is classified Benign in CA5A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-27). AlphaMissense: likely benign (0.108); Common (popmax 7.62%, afr) — too common for a highly-penetrant pathogenic allele; Associated with hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency.

What condition is associated with CA5A p.Asn45Lys (c.135T>A)?

CA5A p.Asn45Lys (c.135T>A) is associated with hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (ClinVar).

What do computational predictors say about CA5A p.Asn45Lys (c.135T>A)?

AlphaMissense predicts likely benign (score 0.108) — an in-silico prediction, not a clinical call.

CA5A p.Asn45Lys

Q: How common is CA5A p.Asn45Lys (c.135T>A) in the general population?

CA5A p.Asn45Lys (c.135T>A) is common (popmax 7.62%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

Q: How is Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.135T>A · rs77325391 · VCV380517

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.108 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 7.62%, afr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency

Computational evidence

Protein change
AlphaMissense	0.108	likely benign
REVEL	0.257	benign-leaning
SaProt	LLR -5.80	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 -1.2	GERP -3.7
Regional constraint	o/e 1.11	unconstrained · MANE · 48 kb · p 0.027 · regional, not allelic
Overall
CADD	0.052	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 7.62% African / African-American · 5,709/74,884 alleles

Filtering AF 7.46% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.39%

Overall 0.42% 6,767/1,612,282 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.62%	13
Ashkenazi Jewishnot grpmax-eligible	0.642%	156
Admixed American	0.564%	177
Remaining individualsnot grpmax-eligible	0.56%	178
Middle Eastern	0.347%	288
European (non-Finnish)	0.0126%	7,963
South Asian	0.0121%	8,275

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: CA5A
Protein: p.Asn45Lys
Coding: c.135T>A
MANE Select: NM_001739
dbSNP: rs77325391
Type: single nucleotide variant
Location: chr16:87936316 (GRCh38)
Gene constraint: LOEUF 1.257 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.38
Residue 45: the alpha-carbonic anhydrase domain

Full CA5A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal

Similar variants

CA5A p.Arg32Ter Pathogenic ★★ same condition
CA5A p.Glu241Lys Pathogenic/Likely pathogenic ★★ same condition
CA5A p.Ala149Thr Uncertain significance ★★ ⚠ same condition
CA5A p.Ala208Val Uncertain significance ★★ ⚠ same condition
CA5A p.Ala261Val Uncertain significance ★★ ⚠ same condition
CA5A p.Arg26His Uncertain significance ★★ ⚠ same condition
CA5A p.Asp216Ala Uncertain significance ★★ ⚠ same condition
CA5A p.Gln79Glu 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/ca5a-p-asn45lys (accessed [today's date]).

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